diff --git a/packages/react-native/ReactCommon/react/renderer/mounting/Differentiator.cpp b/packages/react-native/ReactCommon/react/renderer/mounting/Differentiator.cpp
index b76a03881be6..41de087d3f80 100644
--- a/packages/react-native/ReactCommon/react/renderer/mounting/Differentiator.cpp
+++ b/packages/react-native/ReactCommon/react/renderer/mounting/Differentiator.cpp
@@ -708,9 +708,9 @@ static void calculateShadowViewMutationsFlattener(
             auto unvisitedOtherNodesIt =
                 unvisitedOtherNodes.find(newChild.shadowView.tag);
             if (unvisitedOtherNodesIt != unvisitedOtherNodes.end()) {
-              auto unvisitedItPair = *unvisitedOtherNodesIt->second;
+              auto* unvisitedItPair = unvisitedOtherNodesIt->second;
               unvisitedRecursiveChildPairs.insert(
-                  {unvisitedItPair.shadowView.tag, &unvisitedItPair});
+                  {unvisitedItPair->shadowView.tag, unvisitedItPair});
             } else {
               unvisitedRecursiveChildPairs.insert(
                   {newChild.shadowView.tag, &newChild});
@@ -820,6 +820,9 @@ static void calculateShadowViewMutationsFlattener(
   // Final step: go through creation/deletion candidates and delete/create
   // subtrees if they were never visited during the execution of the above
   // loop and recursions.
+  const auto& subVisitedMap = reparentMode == ReparentMode::Flatten
+      ? *subVisitedOldMap
+      : *subVisitedNewMap;
   for (auto& deletionCreationCandidatePair : deletionCreationCandidatePairs) {
     auto& treeChildPair = *deletionCreationCandidatePair.second;
 
@@ -828,7 +831,10 @@ static void calculateShadowViewMutationsFlattener(
     // already created/deleted and we don't need to do that here.
     // It is always the responsibility of the matcher to update subtrees when
     // nodes are matched.
-    if (treeChildPair.inOtherTree()) {
+    // The recursion can match the node through a different pair instance
+    // (e.g. when zIndex orders it before its parent), so check its tag too.
+    if (treeChildPair.inOtherTree() ||
+        subVisitedMap.contains(treeChildPair.shadowView.tag)) {
       continue;
     }
 
diff --git a/packages/react-native/src/private/renderer/mounting/__tests__/Mounting-itest.js b/packages/react-native/src/private/renderer/mounting/__tests__/Mounting-itest.js
index affe86ef97bb..c260930ad584 100644
--- a/packages/react-native/src/private/renderer/mounting/__tests__/Mounting-itest.js
+++ b/packages/react-native/src/private/renderer/mounting/__tests__/Mounting-itest.js
@@ -446,6 +446,73 @@ describe('ViewFlattening', () => {
       />,
     );
   });
+
+  test('#58647: child with negative zIndex is kept when its parent flattens and its grandparent unflattens', () => {
+    const root = Fantom.createRoot();
+
+    function render(opacityOnGrandparent: boolean) {
+      Fantom.runTask(() => {
+        root.render(
+          <View nativeID="Q" style={{opacity: 0.5}}>
+            <View style={opacityOnGrandparent ? {opacity: 0.5} : null}>
+              <View style={opacityOnGrandparent ? null : {opacity: 0.5}}>
+                <View nativeID="A" />
+                <View nativeID="K" style={{zIndex: -1}} />
+                <View nativeID="B" />
+              </View>
+            </View>
+          </View>,
+        );
+      });
+    }
+
+    const expectedOutput = (
+      <rn-view nativeID="Q">
+        <rn-view>
+          <rn-view key="0" nativeID="K" />
+          <rn-view key="1" nativeID="A" />
+          <rn-view key="2" nativeID="B" />
+        </rn-view>
+      </rn-view>
+    );
+
+    render(false);
+    root.takeMountingManagerLogs();
+
+    render(true);
+    expect(root.takeMountingManagerLogs()).toEqual([
+      'Remove {type: "View", parentNativeID: "Q", index: 0, nativeID: (N/A)}',
+      'Remove {type: "View", parentNativeID: (N/A), index: 2, nativeID: "B"}',
+      'Remove {type: "View", parentNativeID: (N/A), index: 1, nativeID: "A"}',
+      'Remove {type: "View", parentNativeID: (N/A), index: 0, nativeID: "K"}',
+      'Delete {type: "View", nativeID: (N/A)}',
+      'Create {type: "View", nativeID: (N/A)}',
+      'Insert {type: "View", parentNativeID: "Q", index: 0, nativeID: (N/A)}',
+      'Insert {type: "View", parentNativeID: (N/A), index: 0, nativeID: "K"}',
+      'Insert {type: "View", parentNativeID: (N/A), index: 1, nativeID: "A"}',
+      'Insert {type: "View", parentNativeID: (N/A), index: 2, nativeID: "B"}',
+    ]);
+    expect(root.getRenderedOutput({props: ['nativeID']}).toJSX()).toEqual(
+      expectedOutput,
+    );
+
+    render(false);
+    expect(root.takeMountingManagerLogs()).toEqual([
+      'Remove {type: "View", parentNativeID: (N/A), index: 2, nativeID: "B"}',
+      'Remove {type: "View", parentNativeID: (N/A), index: 1, nativeID: "A"}',
+      'Remove {type: "View", parentNativeID: (N/A), index: 0, nativeID: "K"}',
+      'Remove {type: "View", parentNativeID: "Q", index: 0, nativeID: (N/A)}',
+      'Delete {type: "View", nativeID: (N/A)}',
+      'Create {type: "View", nativeID: (N/A)}',
+      'Insert {type: "View", parentNativeID: (N/A), index: 0, nativeID: "K"}',
+      'Insert {type: "View", parentNativeID: (N/A), index: 1, nativeID: "A"}',
+      'Insert {type: "View", parentNativeID: (N/A), index: 2, nativeID: "B"}',
+      'Insert {type: "View", parentNativeID: "Q", index: 0, nativeID: (N/A)}',
+    ]);
+    expect(root.getRenderedOutput({props: ['nativeID']}).toJSX()).toEqual(
+      expectedOutput,
+    );
+  });
 });
 
 describe('reconciliation of setNativeProps and React commit', () => {