diff --git a/scripts/import-cycles.ts b/scripts/import-cycles.ts
index ee0cd144d5..4ceb3c5973 100644
--- a/scripts/import-cycles.ts
+++ b/scripts/import-cycles.ts
@@ -1,4 +1,4 @@
-import { readdirSync, readFileSync, writeFileSync } from "node:fs";
+import { readdirSync, readFileSync, realpathSync, writeFileSync } from "node:fs";
 import { dirname, join, relative, resolve, sep } from "node:path";
 
 /**
@@ -74,6 +74,8 @@ export function staticImports(source: string, tsx = false): string[] {
 }
 
 export function scanGraph(root: string, sourceRoot = SOURCE_ROOT): ImportGraph {
+  // Bun resolves imports to physical paths; graph keys must use the same root (e.g. /var on macOS).
+  root = realpathSync(root);
   const graph: ImportGraph = new Map();
   for (const abs of listSources(join(root, sourceRoot)).sort()) {
     const targets = new Set<string>();
diff --git a/structure/overview.md b/structure/overview.md
index f5cab64283..4fccbfab9b 100644
--- a/structure/overview.md
+++ b/structure/overview.md
@@ -138,7 +138,8 @@ still cover the rule, which is a judgement only review makes.
   request-path entrypoints sit on no cycle at all. Type-only imports and dynamic `import()` form no
   edge, so deferring an edge behind `import()` is a sanctioned way to break a loop (issue #6386).
   Bun parses the declarations and resolves local file and directory imports, preserving compact
-  syntax, erased type-only specifiers, and the runtime's TypeScript index-file precedence.
+  syntax, erased type-only specifiers, and the runtime's TypeScript index-file precedence. The
+  scanner canonicalizes the root so symlinked roots and resolved imports share graph identities.
   Enforced by `tests/ci-workflows/import-cycle-ratchet.test.ts`.
 - **INV-RESTORE-01** — `ocx restore` restores native Codex from the pristine catalog with
   retired bare/account-qualified native rows omitted from the output; the original backup stays
diff --git a/tests/ci-workflows/import-cycle-ratchet.test.ts b/tests/ci-workflows/import-cycle-ratchet.test.ts
index 64aeb402dc..9f8378991c 100644
--- a/tests/ci-workflows/import-cycle-ratchet.test.ts
+++ b/tests/ci-workflows/import-cycle-ratchet.test.ts
@@ -1,5 +1,5 @@
 import { describe, expect, test } from "bun:test";
-import { mkdirSync, mkdtempSync, writeFileSync } from "node:fs";
+import { mkdirSync, mkdtempSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { basename, join } from "node:path";
 import {
@@ -69,6 +69,25 @@ describe("import-cycle ratchet: scanner", () => {
     expect(scanGraph(root).get("src/a.ts")).toEqual([`src/nested/${resolved}`]);
   });
 
+  test.each(["ts", "tsx", "mts"])("symlinked roots preserve index.%s cycle identities", extension => {
+    const base = mkdtempSync(join(tmpdir(), "ocx-import-symlink-"));
+    const physical = join(base, "physical");
+    const root = join(base, "alias");
+    try {
+      mkdirSync(join(physical, "src", "nested"), { recursive: true });
+      writeFileSync(join(physical, "src", "a.ts"), 'import { b } from "./nested"; export const a = b;');
+      writeFileSync(join(physical, "src", "nested", `index.${extension}`),
+        'import { a } from "../a"; export const b = a;' + (extension === "tsx" ? " export const view = <span/>;" : ""));
+      symlinkSync(physical, root, process.platform === "win32" ? "junction" : "dir");
+      const graph = scanGraph(root);
+      expect(graph.get("src/a.ts")).toEqual([`src/nested/index.${extension}`]);
+      expect(graph.get(`src/nested/index.${extension}`)).toEqual(["src/a.ts"]);
+      expect(cyclicModules(graph)).toEqual(["src/a.ts", `src/nested/index.${extension}`]);
+    } finally {
+      rmSync(base, { recursive: true, force: true });
+    }
+  });
+
   test("only load-time value imports form edges", () => {
     const source = [
       'import { a } from "./a";',