diff --git a/.changeset/breezy-gorillas-accept.md b/.changeset/breezy-gorillas-accept.md
new file mode 100644
index 00000000..920cfac7
--- /dev/null
+++ b/.changeset/breezy-gorillas-accept.md
@@ -0,0 +1,7 @@
+---
+'@xyflow/react': minor
+'@xyflow/svelte': minor
+'@xyflow/system': patch
+---
+
+Add `zIndexMode` to control how z-index is calculated for nodes and edges
diff --git a/examples/react/src/App/routes.ts b/examples/react/src/App/routes.ts
index 4cf4b57b..055dc9e1 100644
--- a/examples/react/src/App/routes.ts
+++ b/examples/react/src/App/routes.ts
@@ -60,6 +60,7 @@ import DevTools from '../examples/DevTools';
 import Redux from '../examples/Redux';
 import MovingHandles from '../examples/MovingHandles';
 import DetachedHandle from '../examples/DetachedHandle';
+import ZIndexMode from '../examples/ZIndexMode';
 import Middlewares from '../examples/Middlewares';
 
 export interface IRoute {
@@ -384,6 +385,11 @@ const routes: IRoute[] = [
     path: 'use-key-press',
     component: UseKeyPress,
   },
+  {
+    name: 'zIndexMode',
+    path: 'z-index-mode',
+    component: ZIndexMode,
+  },
 ];
 
 export default routes;
diff --git a/examples/react/src/examples/ColorMode/index.tsx b/examples/react/src/examples/ColorMode/index.tsx
index eae8ad86..f867c650 100644
--- a/examples/react/src/examples/ColorMode/index.tsx
+++ b/examples/react/src/examples/ColorMode/index.tsx
@@ -15,8 +15,6 @@ import {
   Position,
 } from '@xyflow/react';
 
-import './style.css';
-
 const nodeDefaults = {
   sourcePosition: Position.Right,
   targetPosition: Position.Left,
diff --git a/examples/react/src/examples/ColorMode/style.css b/examples/react/src/examples/ColorMode/style.css
deleted file mode 100644
index e69de29b..00000000
diff --git a/examples/react/src/examples/ZIndexMode/index.tsx b/examples/react/src/examples/ZIndexMode/index.tsx
new file mode 100644
index 00000000..5b5477d9
--- /dev/null
+++ b/examples/react/src/examples/ZIndexMode/index.tsx
@@ -0,0 +1,88 @@
+import { ChangeEventHandler, useCallback, useState } from 'react';
+import {
+  ReactFlow,
+  addEdge,
+  Node,
+  useNodesState,
+  useEdgesState,
+  OnConnect,
+  Edge,
+  MiniMap,
+  Background,
+  Controls,
+  Position,
+  ZIndexMode,
+  Panel,
+} from '@xyflow/react';
+
+const nodeDefaults = {
+  sourcePosition: Position.Right,
+  targetPosition: Position.Left,
+};
+
+const initialNodes: Node[] = [
+  { id: 'A', type: 'input', position: { x: 0, y: 150 }, data: { label: 'A' }, ...nodeDefaults },
+  { id: 'B', position: { x: 250, y: 0 }, data: { label: 'B' }, ...nodeDefaults },
+  { id: 'C', position: { x: 250, y: 150 }, data: { label: 'C' }, ...nodeDefaults },
+
+  // group 1
+  { id: 'D', position: { x: 0, y: 300 }, width: 200, height: 200, data: { label: 'D' }, ...nodeDefaults },
+  { id: 'E', parentId: 'D', position: { x: 10, y: 10 }, data: { label: 'E' }, ...nodeDefaults },
+
+  // group 2
+  { id: 'F', position: { x: 250, y: 300 }, width: 200, height: 200, data: { label: 'F' }, ...nodeDefaults },
+  { id: 'G', parentId: 'F', position: { x: 10, y: 10 }, data: { label: 'G' }, ...nodeDefaults },
+
+  // group 3
+  { id: 'H', position: { x: 500, y: 300 }, width: 200, height: 200, data: { label: 'H' }, ...nodeDefaults },
+  { id: 'I', parentId: 'H', position: { x: 10, y: 10 }, data: { label: 'I' }, ...nodeDefaults },
+];
+
+const initialEdges: Edge[] = [
+  {
+    id: 'A-B',
+    source: 'A',
+    target: 'B',
+  },
+  {
+    id: 'A-C',
+    source: 'A',
+    target: 'C',
+  },
+];
+
+function ZIndexModeFlow() {
+  const [zIndexMode, setZIndexMode] = useState<ZIndexMode>('auto');
+  const [nodes, , onNodesChange] = useNodesState(initialNodes);
+  const [edges, setEdges, onEdgesChange] = useEdgesState(initialEdges);
+
+  const onConnect: OnConnect = useCallback((params) => setEdges((eds) => addEdge(params, eds)), [setEdges]);
+
+  const onChange: ChangeEventHandler<HTMLSelectElement> = (evt) => setZIndexMode(evt.target.value as ZIndexMode);
+
+  return (
+    <ReactFlow
+      nodes={nodes}
+      edges={edges}
+      onNodesChange={onNodesChange}
+      onEdgesChange={onEdgesChange}
+      onConnect={onConnect}
+      zIndexMode={zIndexMode}
+      fitView
+    >
+      <MiniMap />
+      <Background />
+      <Controls />
+
+      <Panel position="top-right">
+        <select value={zIndexMode} onChange={onChange} data-testid="zindexmode-select">
+          <option value="manual">manual</option>
+          <option value="basic">basic</option>
+          <option value="auto">auto</option>
+        </select>
+      </Panel>
+    </ReactFlow>
+  );
+}
+
+export default ZIndexModeFlow;
diff --git a/packages/react/src/components/EdgeWrapper/index.tsx b/packages/react/src/components/EdgeWrapper/index.tsx
index 7b76cdfa..700ef11a 100644
--- a/packages/react/src/components/EdgeWrapper/index.tsx
+++ b/packages/react/src/components/EdgeWrapper/index.tsx
@@ -89,6 +89,7 @@ function EdgeWrapper<EdgeType extends Edge = Edge>({
           sourceNode,
           targetNode,
           elevateOnSelect: store.elevateEdgesOnSelect,
+          zIndexMode: store.zIndexMode,
         });
 
         return {
diff --git a/packages/react/src/components/ReactFlowProvider/index.tsx b/packages/react/src/components/ReactFlowProvider/index.tsx
index 11a9c6b8..51d344f0 100644
--- a/packages/react/src/components/ReactFlowProvider/index.tsx
+++ b/packages/react/src/components/ReactFlowProvider/index.tsx
@@ -4,7 +4,7 @@ import { Provider } from '../../contexts/StoreContext';
 import { createStore } from '../../store';
 import { BatchProvider } from '../BatchProvider';
 import type { Node, Edge, FitViewOptions } from '../../types';
-import { CoordinateExtent, NodeOrigin } from '@xyflow/system';
+import { CoordinateExtent, NodeOrigin, ZIndexMode } from '@xyflow/system';
 
 export type ReactFlowProviderProps = {
   /** These nodes are used to initialize the flow. They are not dynamic. */
@@ -48,6 +48,7 @@ export type ReactFlowProviderProps = {
    */
   nodeExtent?: CoordinateExtent;
   children: ReactNode;
+  zIndexMode?: ZIndexMode;
 };
 
 /**
@@ -97,6 +98,7 @@ export function ReactFlowProvider({
   fitView,
   nodeOrigin,
   nodeExtent,
+  zIndexMode,
   children,
 }: ReactFlowProviderProps) {
   const [store] = useState(() =>
@@ -113,6 +115,7 @@ export function ReactFlowProvider({
       fitViewOptions,
       nodeOrigin,
       nodeExtent,
+      zIndexMode,
     })
   );
 
diff --git a/packages/react/src/components/StoreUpdater/index.tsx b/packages/react/src/components/StoreUpdater/index.tsx
index 7f375d0a..223e62bc 100644
--- a/packages/react/src/components/StoreUpdater/index.tsx
+++ b/packages/react/src/components/StoreUpdater/index.tsx
@@ -70,6 +70,7 @@ const reactFlowFieldsToTrack = [
   'debug',
   'autoPanSpeed',
   'ariaLabelConfig',
+  'zIndexMode',
 ] as const;
 
 type ReactFlowFieldsToTrack = (typeof reactFlowFieldsToTrack)[number];
diff --git a/packages/react/src/container/ReactFlow/Wrapper.tsx b/packages/react/src/container/ReactFlow/Wrapper.tsx
index 9ae0aa62..0591aba3 100644
--- a/packages/react/src/container/ReactFlow/Wrapper.tsx
+++ b/packages/react/src/container/ReactFlow/Wrapper.tsx
@@ -3,7 +3,7 @@ import { useContext, type ReactNode } from 'react';
 import StoreContext from '../../contexts/StoreContext';
 import { ReactFlowProvider } from '../../components/ReactFlowProvider';
 import type { Node, Edge, FitViewOptions } from '../../types';
-import { CoordinateExtent, NodeOrigin } from '@xyflow/system';
+import { CoordinateExtent, NodeOrigin, ZIndexMode } from '@xyflow/system';
 
 export function Wrapper({
   children,
@@ -19,6 +19,7 @@ export function Wrapper({
   maxZoom,
   nodeOrigin,
   nodeExtent,
+  zIndexMode,
 }: {
   children: ReactNode;
   nodes?: Node[];
@@ -33,6 +34,7 @@ export function Wrapper({
   maxZoom?: number;
   nodeOrigin?: NodeOrigin;
   nodeExtent?: CoordinateExtent;
+  zIndexMode?: ZIndexMode;
 }) {
   const isWrapped = useContext(StoreContext);
 
@@ -58,6 +60,7 @@ export function Wrapper({
       initialMaxZoom={maxZoom}
       nodeOrigin={nodeOrigin}
       nodeExtent={nodeExtent}
+      zIndexMode={zIndexMode}
     >
       {children}
     </ReactFlowProvider>
diff --git a/packages/react/src/container/ReactFlow/index.tsx b/packages/react/src/container/ReactFlow/index.tsx
index f01af831..b04f2955 100644
--- a/packages/react/src/container/ReactFlow/index.tsx
+++ b/packages/react/src/container/ReactFlow/index.tsx
@@ -127,8 +127,8 @@ function ReactFlow<NodeType extends Node = Node, EdgeType extends Edge = Edge>(
     attributionPosition,
     proOptions,
     defaultEdgeOptions,
-    elevateNodesOnSelect,
-    elevateEdgesOnSelect,
+    elevateNodesOnSelect = true,
+    elevateEdgesOnSelect = false,
     disableKeyboardA11y = false,
     autoPanOnConnect,
     autoPanOnNodeDrag,
@@ -148,6 +148,7 @@ function ReactFlow<NodeType extends Node = Node, EdgeType extends Edge = Edge>(
     debug,
     onScroll,
     ariaLabelConfig,
+    zIndexMode = 'basic',
     ...rest
   }: ReactFlowProps<NodeType, EdgeType>,
   ref: ForwardedRef<HTMLDivElement>
@@ -186,6 +187,7 @@ function ReactFlow<NodeType extends Node = Node, EdgeType extends Edge = Edge>(
         maxZoom={maxZoom}
         nodeOrigin={nodeOrigin}
         nodeExtent={nodeExtent}
+        zIndexMode={zIndexMode}
       >
         <GraphView<NodeType, EdgeType>
           onInit={onInit}
@@ -311,6 +313,7 @@ function ReactFlow<NodeType extends Node = Node, EdgeType extends Edge = Edge>(
           onBeforeDelete={onBeforeDelete}
           debug={debug}
           ariaLabelConfig={ariaLabelConfig}
+          zIndexMode={zIndexMode}
         />
         <SelectionListener<NodeType, EdgeType> onSelectionChange={onSelectionChange} />
         {children}
diff --git a/packages/react/src/index.ts b/packages/react/src/index.ts
index f251ba5d..79a50440 100644
--- a/packages/react/src/index.ts
+++ b/packages/react/src/index.ts
@@ -116,6 +116,7 @@ export {
   type SetViewport,
   type FitBounds,
   type HandleConnection,
+  type ZIndexMode,
 } from '@xyflow/system';
 
 // we need this workaround to prevent a duplicate identifier error
diff --git a/packages/react/src/store/index.ts b/packages/react/src/store/index.ts
index fa1b5e3d..1c5bdd3d 100644
--- a/packages/react/src/store/index.ts
+++ b/packages/react/src/store/index.ts
@@ -16,6 +16,7 @@ import {
   fitViewport,
   getHandlePosition,
   Position,
+  ZIndexMode
 } from '@xyflow/system';
 
 import { applyEdgeChanges, applyNodeChanges, createSelectionChange, getSelectionChanges } from '../utils/changes';
@@ -35,6 +36,7 @@ const createStore = ({
   maxZoom,
   nodeOrigin,
   nodeExtent,
+  zIndexMode,
 }: {
   nodes?: Node[];
   edges?: Edge[];
@@ -48,6 +50,7 @@ const createStore = ({
   maxZoom?: number;
   nodeOrigin?: NodeOrigin;
   nodeExtent?: CoordinateExtent;
+  zIndexMode?: ZIndexMode;
 }) =>
   createWithEqualityFn<ReactFlowState>((set, get) => {
     async function resolveFitView() {
@@ -91,9 +94,10 @@ const createStore = ({
         nodeExtent,
         defaultNodes,
         defaultEdges,
+        zIndexMode,
       }),
       setNodes: (nodes: Node[]) => {
-        const { nodeLookup, parentLookup, nodeOrigin, elevateNodesOnSelect, fitViewQueued } = get();
+        const { nodeLookup, parentLookup, nodeOrigin, elevateNodesOnSelect, fitViewQueued, zIndexMode } = get();
         /*
          * setNodes() is called exclusively in response to user actions:
          * - either when the `<ReactFlow nodes>` prop is updated in the controlled ReactFlow setup,
@@ -108,6 +112,7 @@ const createStore = ({
           nodeExtent,
           elevateNodesOnSelect,
           checkEquality: true,
+          zIndexMode,
         });
 
         if (fitViewQueued && nodesInitialized) {
@@ -142,8 +147,17 @@ const createStore = ({
        * new dimensions and update the nodes.
        */
       updateNodeInternals: (updates) => {
-        const { triggerNodeChanges, nodeLookup, parentLookup, domNode, nodeOrigin, nodeExtent, debug, fitViewQueued } =
-          get();
+        const {
+          triggerNodeChanges,
+          nodeLookup,
+          parentLookup,
+          domNode,
+          nodeOrigin,
+          nodeExtent,
+          debug,
+          fitViewQueued,
+          zIndexMode,
+        } = get();
 
         const { changes, updatedInternals } = updateNodeInternalsSystem(
           updates,
@@ -151,14 +165,15 @@ const createStore = ({
           parentLookup,
           domNode,
           nodeOrigin,
-          nodeExtent
+          nodeExtent,
+          zIndexMode
         );
 
         if (!updatedInternals) {
           return;
         }
 
-        updateAbsolutePositions(nodeLookup, parentLookup, { nodeOrigin, nodeExtent });
+        updateAbsolutePositions(nodeLookup, parentLookup, { nodeOrigin, nodeExtent, zIndexMode });
 
         if (fitViewQueued) {
           resolveFitView();
@@ -343,7 +358,7 @@ const createStore = ({
         triggerEdgeChanges(edgeChanges);
       },
       setNodeExtent: (nextNodeExtent) => {
-        const { nodes, nodeLookup, parentLookup, nodeOrigin, elevateNodesOnSelect, nodeExtent } = get();
+        const { nodes, nodeLookup, parentLookup, nodeOrigin, elevateNodesOnSelect, nodeExtent, zIndexMode } = get();
 
         if (
           nextNodeExtent[0][0] === nodeExtent[0][0] &&
@@ -359,6 +374,7 @@ const createStore = ({
           nodeExtent: nextNodeExtent,
           elevateNodesOnSelect,
           checkEquality: false,
+          zIndexMode,
         });
 
         set({ nodeExtent: nextNodeExtent });
diff --git a/packages/react/src/store/initialState.ts b/packages/react/src/store/initialState.ts
index c7ddda17..26a5c045 100644
--- a/packages/react/src/store/initialState.ts
+++ b/packages/react/src/store/initialState.ts
@@ -11,6 +11,7 @@ import {
   initialConnection,
   CoordinateExtent,
   defaultAriaLabelConfig,
+  ZIndexMode,
 } from '@xyflow/system';
 
 import type { Edge, FitViewOptions, InternalNode, Node, ReactFlowStore } from '../types';
@@ -28,6 +29,7 @@ const getInitialState = ({
   maxZoom = 2,
   nodeOrigin,
   nodeExtent,
+  zIndexMode = 'basic',
 }: {
   nodes?: Node[];
   edges?: Edge[];
@@ -41,6 +43,7 @@ const getInitialState = ({
   maxZoom?: number;
   nodeOrigin?: NodeOrigin;
   nodeExtent?: CoordinateExtent;
+  zIndexMode?: ZIndexMode;
 } = {}): ReactFlowStore => {
   const nodeLookup = new Map<string, InternalNode>();
   const parentLookup = new Map();
@@ -56,7 +59,7 @@ const getInitialState = ({
   const nodesInitialized = adoptUserNodes(storeNodes, nodeLookup, parentLookup, {
     nodeOrigin: storeNodeOrigin,
     nodeExtent: storeNodeExtent,
-    elevateNodesOnSelect: false,
+    zIndexMode,
   });
 
   let transform: Transform = [0, 0, 1];
@@ -119,7 +122,7 @@ const getInitialState = ({
     edgesReconnectable: true,
     elementsSelectable: true,
     elevateNodesOnSelect: true,
-    elevateEdgesOnSelect: false,
+    elevateEdgesOnSelect: true,
     selectNodesOnDrag: true,
 
     multiSelectionActive: false,
@@ -146,6 +149,7 @@ const getInitialState = ({
     lib: 'react',
     debug: false,
     ariaLabelConfig: defaultAriaLabelConfig,
+    zIndexMode,
 
     onNodesChangeMiddlewareMap: new Map(),
     onEdgesChangeMiddlewareMap: new Map(),
diff --git a/packages/react/src/types/component-props.ts b/packages/react/src/types/component-props.ts
index 3e534aaa..effc7ca6 100644
--- a/packages/react/src/types/component-props.ts
+++ b/packages/react/src/types/component-props.ts
@@ -23,6 +23,7 @@ import type {
   OnReconnect,
   AriaLabelConfig,
   FinalConnectionState,
+  ZIndexMode,
 } from '@xyflow/system';
 
 import type {
@@ -691,4 +692,11 @@ export interface ReactFlowProps<NodeType extends Node = Node, EdgeType extends E
    * Allows localization, customization of ARIA descriptions, control labels, minimap labels, and other UI strings.
    */
   ariaLabelConfig?: Partial<AriaLabelConfig>;
+  /**
+   * Used to define how z-indexing is calculated for nodes and edges.
+   * 'auto' is for selections and sub flows, 'basic' for selections only, and 'manual' for no auto z-indexing.
+   *
+   * @default 'basic'
+   */
+  zIndexMode?: ZIndexMode;
 }
diff --git a/packages/react/src/types/store.ts b/packages/react/src/types/store.ts
index 717961ec..db881fc2 100644
--- a/packages/react/src/types/store.ts
+++ b/packages/react/src/types/store.ts
@@ -29,7 +29,8 @@ import {
   type EdgeChange,
   type ParentLookup,
   type AriaLabelConfig,
-  SetCenter,
+  type SetCenter,
+  type ZIndexMode,
 } from '@xyflow/system';
 
 import type {
@@ -153,6 +154,7 @@ export type ReactFlowStore<NodeType extends Node = Node, EdgeType extends Edge =
   debug: boolean;
   ariaLabelConfig: AriaLabelConfig;
 
+  zIndexMode: ZIndexMode;
   onNodesChangeMiddlewareMap: Map<symbol, (changes: NodeChange<NodeType>[]) => NodeChange<NodeType>[]>;
   onEdgesChangeMiddlewareMap: Map<symbol, (changes: EdgeChange<EdgeType>[]) => EdgeChange<EdgeType>[]>;
 };
diff --git a/packages/svelte/src/lib/container/SvelteFlow/SvelteFlow.svelte b/packages/svelte/src/lib/container/SvelteFlow/SvelteFlow.svelte
index ab9378b8..a2283be7 100644
--- a/packages/svelte/src/lib/container/SvelteFlow/SvelteFlow.svelte
+++ b/packages/svelte/src/lib/container/SvelteFlow/SvelteFlow.svelte
@@ -75,7 +75,7 @@
   }: SvelteFlowProps<NodeType, EdgeType> &
     Omit<HTMLAttributes<HTMLDivElement>, 'onselectionchange'> = $props();
 
-  // svelte-ignore non_reactive_update
+  // svelte-ignore non_reactive_update, state_referenced_locally
   let store = createStore<NodeType, EdgeType>({
     props,
     width,
diff --git a/packages/svelte/src/lib/container/SvelteFlow/Wrapper.svelte b/packages/svelte/src/lib/container/SvelteFlow/Wrapper.svelte
index 88ba9f1a..b9314774 100644
--- a/packages/svelte/src/lib/container/SvelteFlow/Wrapper.svelte
+++ b/packages/svelte/src/lib/container/SvelteFlow/Wrapper.svelte
@@ -96,6 +96,7 @@
     ariaLabelConfig,
     autoPanSpeed,
     panOnScrollSpeed,
+    zIndexMode,
     ...divAttributes
   } = $derived(rest);
   /* eslint-enable @typescript-eslint/no-unused-vars */
diff --git a/packages/svelte/src/lib/container/SvelteFlow/types.ts b/packages/svelte/src/lib/container/SvelteFlow/types.ts
index 0fbd4b18..8e5c6c8c 100644
--- a/packages/svelte/src/lib/container/SvelteFlow/types.ts
+++ b/packages/svelte/src/lib/container/SvelteFlow/types.ts
@@ -21,7 +21,8 @@ import type {
   OnReconnect,
   OnReconnectStart,
   OnReconnectEnd,
-  AriaLabelConfig
+  AriaLabelConfig,
+  ZIndexMode
 } from '@xyflow/system';
 
 import type {
@@ -500,4 +501,11 @@ export type SvelteFlowProps<
      * Allows localization, customization of ARIA descriptions, control labels, minimap labels, and other UI strings.
      */
     ariaLabelConfig?: Partial<AriaLabelConfig>;
+    /**
+     * Used to define how z-indexing is calculated for nodes and edges.
+     * 'auto' is for selections and sub flows, 'basic' for selections only, and 'manual' for no auto z-indexing.
+     *
+     * @default 'basic'
+     */
+    zIndexMode?: ZIndexMode;
   };
diff --git a/packages/svelte/src/lib/index.ts b/packages/svelte/src/lib/index.ts
index 815803f7..9665f211 100644
--- a/packages/svelte/src/lib/index.ts
+++ b/packages/svelte/src/lib/index.ts
@@ -122,7 +122,8 @@ export {
   type SetCenter,
   type SetViewport,
   type FitBounds,
-  type HandleConnection
+  type HandleConnection,
+  type ZIndexMode
 } from '@xyflow/system';
 
 // system utils
diff --git a/packages/svelte/src/lib/store/index.ts b/packages/svelte/src/lib/store/index.ts
index 30bcafc1..3a7b1123 100644
--- a/packages/svelte/src/lib/store/index.ts
+++ b/packages/svelte/src/lib/store/index.ts
@@ -73,7 +73,9 @@ export function createStore<NodeType extends Node = Node, EdgeType extends Edge
       store.nodeLookup,
       store.parentLookup,
       store.domNode,
-      store.nodeOrigin
+      store.nodeOrigin,
+      store.nodeExtent,
+      store.zIndexMode
     );
 
     if (!updatedInternals) {
@@ -82,7 +84,8 @@ export function createStore<NodeType extends Node = Node, EdgeType extends Edge
 
     updateAbsolutePositions(store.nodeLookup, store.parentLookup, {
       nodeOrigin: store.nodeOrigin,
-      nodeExtent: store.nodeExtent
+      nodeExtent: store.nodeExtent,
+      zIndexMode: store.zIndexMode
     });
 
     if (store.fitViewQueued) {
diff --git a/packages/svelte/src/lib/store/initial-store.svelte.ts b/packages/svelte/src/lib/store/initial-store.svelte.ts
index 9016972c..fb7dfc99 100644
--- a/packages/svelte/src/lib/store/initial-store.svelte.ts
+++ b/packages/svelte/src/lib/store/initial-store.svelte.ts
@@ -36,7 +36,8 @@ import {
   type OnReconnect,
   type OnReconnectStart,
   type OnReconnectEnd,
-  type AriaLabelConfig
+  type AriaLabelConfig,
+  type ZIndexMode
 } from '@xyflow/system';
 
 import DefaultNode from '$lib/components/nodes/DefaultNode.svelte';
@@ -116,13 +117,15 @@ export function getInitialStore<NodeType extends Node = Node, EdgeType extends E
     panZoom: PanZoomInstance | null = $state.raw(null);
     width = $state.raw<number>(signals.width ?? 0);
     height = $state.raw<number>(signals.height ?? 0);
+    zIndexMode = $state.raw<ZIndexMode>(signals.props.zIndexMode ?? 'basic');
 
     nodesInitialized: boolean = $derived.by(() => {
       const nodesInitialized = adoptUserNodes(signals.nodes, this.nodeLookup, this.parentLookup, {
         nodeExtent: this.nodeExtent,
         nodeOrigin: this.nodeOrigin,
         elevateNodesOnSelect: signals.props.elevateNodesOnSelect ?? true,
-        checkEquality: true
+        checkEquality: true,
+        zIndexMode: this.zIndexMode
       });
 
       if (this.fitViewQueued && nodesInitialized) {
@@ -226,7 +229,8 @@ export function getInitialStore<NodeType extends Node = Node, EdgeType extends E
         connectionMode,
         onerror,
         onlyRenderVisibleElements,
-        defaultEdgeOptions
+        defaultEdgeOptions,
+        zIndexMode
       } = this;
 
       let visibleNodes: Map<string, InternalNode<NodeType>>;
@@ -239,6 +243,7 @@ export function getInitialStore<NodeType extends Node = Node, EdgeType extends E
         nodeLookup,
         connectionMode,
         elevateEdgesOnSelect: signals.props.elevateEdgesOnSelect ?? true,
+        zIndexMode,
         onerror
       };
 
diff --git a/packages/svelte/src/lib/store/visibleElements.ts b/packages/svelte/src/lib/store/visibleElements.ts
index e8ff8aca..4ef0fa5d 100644
--- a/packages/svelte/src/lib/store/visibleElements.ts
+++ b/packages/svelte/src/lib/store/visibleElements.ts
@@ -7,7 +7,8 @@ import {
   isEdgeVisible,
   type NodeLookup,
   type OnError,
-  type Transform
+  type Transform,
+  type ZIndexMode
 } from '@xyflow/system';
 
 export function getVisibleNodes<NodeType extends Node = Node>(
@@ -42,6 +43,7 @@ export interface EdgeLayoutAllOptions<NodeType extends Node = Node, EdgeType ext
   transform: never;
   width: never;
   height: never;
+  zIndexMode: never;
 }
 
 export interface EdgeLayoutOnlyVisibleOptions<
@@ -53,6 +55,7 @@ export interface EdgeLayoutOnlyVisibleOptions<
   width: number;
   height: number;
   onlyRenderVisible: true;
+  zIndexMode: ZIndexMode;
 }
 
 export type EdgeLayoutOptions<NodeType extends Node = Node, EdgeType extends Edge = Edge> =
@@ -70,7 +73,8 @@ export function getLayoutedEdges<NodeType extends Node = Node, EdgeType extends
     connectionMode,
     onerror,
     onlyRenderVisible,
-    elevateEdgesOnSelect
+    elevateEdgesOnSelect,
+    zIndexMode
   } = options;
   const layoutedEdges = new Map<string, EdgeLayouted<EdgeType>>();
   for (const edge of edges) {
@@ -134,7 +138,8 @@ export function getLayoutedEdges<NodeType extends Node = Node, EdgeType extends
           zIndex: edge.zIndex ?? defaultEdgeOptions.zIndex,
           sourceNode,
           targetNode,
-          elevateOnSelect: elevateEdgesOnSelect
+          elevateOnSelect: elevateEdgesOnSelect,
+          zIndexMode
         }),
         sourceNode,
         targetNode,
diff --git a/packages/system/src/types/general.ts b/packages/system/src/types/general.ts
index d43c50ee..d2939f82 100644
--- a/packages/system/src/types/general.ts
+++ b/packages/system/src/types/general.ts
@@ -367,3 +367,13 @@ export type OnBeforeDeleteBase<NodeType extends NodeBase = NodeBase, EdgeType ex
   nodes: NodeType[];
   edges: EdgeType[];
 }) => Promise<boolean | { nodes: NodeType[]; edges: EdgeType[] }>;
+
+/**
+ * The `ZIndexMode` type is used to define how z-indexing is calculated for nodes and edges.
+ * `auto` mode will automatically manage z-indexing for selections and sub flows.
+ * `basic` mode will only manage z-indexing for selections.
+ * `manual` mode does not apply any automatic z-indexing.
+ *
+ * @public
+ */
+export type ZIndexMode = 'auto' | 'basic' | 'manual';
diff --git a/packages/system/src/utils/edges/general.ts b/packages/system/src/utils/edges/general.ts
index 515a285a..25719c3d 100644
--- a/packages/system/src/utils/edges/general.ts
+++ b/packages/system/src/utils/edges/general.ts
@@ -1,4 +1,13 @@
-import { Connection, InternalNodeBase, Transform, errorMessages, isEdgeBase, EdgeBase } from '../..';
+import {
+  Connection,
+  InternalNodeBase,
+  Transform,
+  errorMessages,
+  isEdgeBase,
+  EdgeBase,
+  ZIndexMode,
+  isManualZIndexMode,
+} from '../..';
 import { getOverlappingArea, boxToRect, nodeToBox, getBoundsOfBoxes, devWarn } from '../general';
 
 // this is used for straight edges and simple smoothstep edges (LTR, RTL, BTT, TTB)
@@ -28,6 +37,7 @@ export type GetEdgeZIndexParams = {
   selected?: boolean;
   zIndex?: number;
   elevateOnSelect?: boolean;
+  zIndexMode?: ZIndexMode;
 };
 
 /**
@@ -41,12 +51,19 @@ export function getElevatedEdgeZIndex({
   selected = false,
   zIndex,
   elevateOnSelect = false,
+  zIndexMode = 'basic',
 }: GetEdgeZIndexParams): number {
+  const manualZIndexMode = isManualZIndexMode(zIndexMode);
+
   if (zIndex !== undefined) {
     return zIndex;
   }
-  const edgeZ = elevateOnSelect && selected ? 1000 : 0;
 
+  if (manualZIndexMode) {
+    return 0;
+  }
+
+  const edgeZ = elevateOnSelect && selected ? 1000 : 0;
   const nodeZ = Math.max(
     sourceNode.parentId || (elevateOnSelect && sourceNode.selected) ? sourceNode.internals.z : 0,
     targetNode.parentId || (elevateOnSelect && targetNode.selected) ? targetNode.internals.z : 0
diff --git a/packages/system/src/utils/store.ts b/packages/system/src/utils/store.ts
index 88f4bb79..b499dfee 100644
--- a/packages/system/src/utils/store.ts
+++ b/packages/system/src/utils/store.ts
@@ -1,4 +1,4 @@
-import { Handle, HandleConnection, infiniteExtent, NodeHandle, NodeHandleBounds } from '..';
+import { Handle, HandleConnection, infiniteExtent, NodeHandleBounds, ZIndexMode } from '..';
 import {
   NodeBase,
   CoordinateExtent,
@@ -37,6 +37,7 @@ const defaultOptions = {
   nodeOrigin: [0, 0] as NodeOrigin,
   nodeExtent: infiniteExtent,
   elevateNodesOnSelect: true,
+  zIndexMode: 'basic' as ZIndexMode,
   defaults: {},
 };
 
@@ -112,21 +113,26 @@ type UpdateNodesOptions<NodeType extends NodeBase> = {
   nodeExtent?: CoordinateExtent;
   elevateNodesOnSelect?: boolean;
   defaults?: Partial<NodeType>;
+  zIndexMode?: ZIndexMode;
   checkEquality?: boolean;
 };
 
+export function isManualZIndexMode(zIndexMode?: ZIndexMode): boolean {
+  return zIndexMode === 'manual';
+}
+
 export function adoptUserNodes<NodeType extends NodeBase>(
   nodes: NodeType[],
   nodeLookup: NodeLookup<InternalNodeBase<NodeType>>,
   parentLookup: ParentLookup<InternalNodeBase<NodeType>>,
-  options?: UpdateNodesOptions<NodeType>
+  options: UpdateNodesOptions<NodeType> = {}
 ): boolean {
   const _options = mergeObjects(adoptUserNodesDefaultOptions, options);
-
-  let rootParentIndex = { i: -1 };
-  let nodesInitialized = nodes.length > 0;
+  const rootParentIndex = { i: 0 };
   const tmpLookup = new Map(nodeLookup);
-  const selectedNodeZ: number = _options?.elevateNodesOnSelect ? SELECTED_NODE_Z : 0;
+  const selectedNodeZ: number =
+    _options?.elevateNodesOnSelect && !isManualZIndexMode(_options.zIndexMode) ? SELECTED_NODE_Z : 0;
+  let nodesInitialized = nodes.length > 0;
 
   nodeLookup.clear();
   parentLookup.clear();
@@ -152,7 +158,7 @@ export function adoptUserNodes<NodeType extends NodeBase>(
           positionAbsolute: clampedPosition,
           // if user re-initializes the node or removes `measured` for whatever reason, we reset the handleBounds so that the node gets re-measured
           handleBounds: parseHandles(userNode, internalNode),
-          z: calculateZ(userNode, selectedNodeZ),
+          z: calculateZ(userNode, selectedNodeZ, _options.zIndexMode),
           userNode,
         },
       };
@@ -201,10 +207,10 @@ function updateChildNode<NodeType extends NodeBase>(
   node: InternalNodeBase<NodeType>,
   nodeLookup: NodeLookup<InternalNodeBase<NodeType>>,
   parentLookup: ParentLookup<InternalNodeBase<NodeType>>,
-  options?: UpdateNodesOptions<NodeType>,
+  options: UpdateNodesOptions<NodeType>,
   rootParentIndex?: { i: number }
 ) {
-  const { elevateNodesOnSelect, nodeOrigin, nodeExtent } = mergeObjects(defaultOptions, options);
+  const { elevateNodesOnSelect, nodeOrigin, nodeExtent, zIndexMode } = mergeObjects(defaultOptions, options);
   const parentId = node.parentId!;
   const parentNode = nodeLookup.get(parentId);
 
@@ -218,7 +224,12 @@ function updateChildNode<NodeType extends NodeBase>(
   updateParentLookup(node, parentLookup);
 
   // We just want to set the rootParentIndex for the first child
-  if (rootParentIndex && !parentNode.parentId && parentNode.internals.rootParentIndex === undefined) {
+  if (
+    rootParentIndex &&
+    !parentNode.parentId &&
+    parentNode.internals.rootParentIndex === undefined &&
+    zIndexMode === 'auto'
+  ) {
     parentNode.internals.rootParentIndex = ++rootParentIndex.i;
     parentNode.internals.z = parentNode.internals.z + rootParentIndex.i * ROOT_PARENT_Z_INCREMENT;
   }
@@ -228,8 +239,8 @@ function updateChildNode<NodeType extends NodeBase>(
     rootParentIndex.i = parentNode.internals.rootParentIndex;
   }
 
-  const selectedNodeZ = elevateNodesOnSelect ? SELECTED_NODE_Z : 0;
-  const { x, y, z } = calculateChildXYZ(node, parentNode, nodeOrigin, nodeExtent, selectedNodeZ);
+  const selectedNodeZ = elevateNodesOnSelect && !isManualZIndexMode(zIndexMode) ? SELECTED_NODE_Z : 0;
+  const { x, y, z } = calculateChildXYZ(node, parentNode, nodeOrigin, nodeExtent, selectedNodeZ, zIndexMode);
   const { positionAbsolute } = node.internals;
   const positionChanged = x !== positionAbsolute.x || y !== positionAbsolute.y;
 
@@ -246,8 +257,14 @@ function updateChildNode<NodeType extends NodeBase>(
   }
 }
 
-function calculateZ(node: NodeBase, selectedNodeZ: number) {
-  return (isNumeric(node.zIndex) ? node.zIndex : 0) + (node.selected ? selectedNodeZ : 0);
+function calculateZ(node: NodeBase, selectedNodeZ: number, zIndexMode: ZIndexMode): number {
+  const zIndex = isNumeric(node.zIndex) ? node.zIndex : 0;
+
+  if (isManualZIndexMode(zIndexMode)) {
+    return zIndex;
+  }
+
+  return zIndex + (node.selected ? selectedNodeZ : 0);
 }
 
 function calculateChildXYZ<NodeType extends NodeBase>(
@@ -255,7 +272,8 @@ function calculateChildXYZ<NodeType extends NodeBase>(
   parentNode: InternalNodeBase<NodeType>,
   nodeOrigin: NodeOrigin,
   nodeExtent: CoordinateExtent,
-  selectedNodeZ: number
+  selectedNodeZ: number,
+  zIndexMode: ZIndexMode
 ) {
   const { x: parentX, y: parentY } = parentNode.internals.positionAbsolute;
   const childDimensions = getNodeDimensions(childNode);
@@ -274,7 +292,7 @@ function calculateChildXYZ<NodeType extends NodeBase>(
     absolutePosition = clampPositionToParent(absolutePosition, childDimensions, parentNode);
   }
 
-  const childZ = calculateZ(childNode, selectedNodeZ);
+  const childZ = calculateZ(childNode, selectedNodeZ, zIndexMode);
   const parentZ = parentNode.internals.z ?? 0;
 
   return {
@@ -378,7 +396,8 @@ export function updateNodeInternals<NodeType extends InternalNodeBase>(
   parentLookup: ParentLookup<NodeType>,
   domNode: HTMLElement | null,
   nodeOrigin?: NodeOrigin,
-  nodeExtent?: CoordinateExtent
+  nodeExtent?: CoordinateExtent,
+  zIndexMode?: ZIndexMode
 ): { changes: (NodeDimensionChange | NodePositionChange)[]; updatedInternals: boolean } {
   const viewportNode = domNode?.querySelector('.xyflow__viewport');
   let updatedInternals = false;
@@ -446,7 +465,7 @@ export function updateNodeInternals<NodeType extends InternalNodeBase>(
       nodeLookup.set(node.id, newNode);
 
       if (node.parentId) {
-        updateChildNode(newNode, nodeLookup, parentLookup, { nodeOrigin });
+        updateChildNode(newNode, nodeLookup, parentLookup, { nodeOrigin, zIndexMode });
       }
 
       updatedInternals = true;