diff --git a/__tests__/worktree-detection.test.ts b/__tests__/worktree-detection.test.ts
new file mode 100644
index 00000000..d0fd934a
--- /dev/null
+++ b/__tests__/worktree-detection.test.ts
@@ -0,0 +1,103 @@
+/**
+ * Git worktree index-mismatch detection (issue #155).
+ *
+ * A CodeGraph index is resolved by walking up to the nearest `.codegraph/`.
+ * When a worktree is nested inside the main checkout, that walk reaches the
+ * MAIN checkout's index and a query silently returns the main branch's code
+ * instead of the worktree's. `detectWorktreeIndexMismatch` spots exactly this
+ * case so callers can warn.
+ *
+ * These tests drive real `git` against real temp worktrees — no mocking — so
+ * they exercise the same `git rev-parse --show-toplevel` behavior production
+ * relies on.
+ */
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { execFileSync } from 'child_process';
+import * as fs from 'fs';
+import * as os from 'os';
+import * as path from 'path';
+import {
+  detectWorktreeIndexMismatch,
+  worktreeMismatchWarning,
+  gitWorktreeRoot,
+} from '../src/sync/worktree';
+
+function git(cwd: string, ...args: string[]): void {
+  execFileSync('git', args, { cwd, stdio: ['ignore', 'ignore', 'ignore'] });
+}
+
+/** realpath so macOS /var → /private/var symlinking doesn't break equality. */
+function real(p: string): string {
+  return fs.realpathSync(path.resolve(p));
+}
+
+describe('detectWorktreeIndexMismatch (issue #155)', () => {
+  let mainRepo: string;   // main checkout — owns the .codegraph index
+  let worktree: string;   // a linked worktree nested inside the main checkout
+  let nonGit: string;     // a directory outside any git repo
+
+  beforeEach(() => {
+    mainRepo = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-wt-main-'));
+    nonGit = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-wt-plain-'));
+
+    git(mainRepo, 'init', '-q');
+    git(mainRepo, 'config', 'user.email', 'test@example.com');
+    git(mainRepo, 'config', 'user.name', 'Test');
+    git(mainRepo, 'config', 'commit.gpgsign', 'false');
+    fs.writeFileSync(path.join(mainRepo, 'README.md'), '# main\n');
+    git(mainRepo, 'add', '.');
+    git(mainRepo, 'commit', '-q', '-m', 'init');
+
+    // Nest the worktree under the main checkout, mirroring tools that place
+    // worktrees in (gitignored) subpaths like `.claude/worktrees/<name>/`.
+    worktree = path.join(mainRepo, 'wt');
+    git(mainRepo, 'worktree', 'add', '-q', '-b', 'feature', worktree);
+  });
+
+  afterEach(() => {
+    try { git(mainRepo, 'worktree', 'remove', '--force', worktree); } catch { /* best effort */ }
+    fs.rmSync(mainRepo, { recursive: true, force: true });
+    fs.rmSync(nonGit, { recursive: true, force: true });
+  });
+
+  it('flags a worktree borrowing the main checkout index', () => {
+    const m = detectWorktreeIndexMismatch(worktree, mainRepo);
+    expect(m).not.toBeNull();
+    expect(m!.worktreeRoot).toBe(real(worktree));
+    expect(m!.indexRoot).toBe(real(mainRepo));
+  });
+
+  it('returns null when the index lives in the same working tree', () => {
+    expect(detectWorktreeIndexMismatch(mainRepo, mainRepo)).toBeNull();
+    expect(detectWorktreeIndexMismatch(worktree, worktree)).toBeNull();
+  });
+
+  it('returns null for a subdirectory of the same working tree', () => {
+    const sub = path.join(mainRepo, 'src');
+    fs.mkdirSync(sub);
+    expect(detectWorktreeIndexMismatch(sub, mainRepo)).toBeNull();
+  });
+
+  it('returns null when startPath is not in a git repo', () => {
+    expect(detectWorktreeIndexMismatch(nonGit, mainRepo)).toBeNull();
+  });
+
+  it('returns null when the index root is a plain (non-worktree) directory', () => {
+    // startPath is a real worktree, but the index sits in an unrelated non-git
+    // dir — that's "index in an ancestor", not "borrowed another worktree".
+    expect(detectWorktreeIndexMismatch(worktree, nonGit)).toBeNull();
+  });
+
+  it('gitWorktreeRoot reports each tree distinctly', () => {
+    expect(gitWorktreeRoot(worktree)).toBe(real(worktree));
+    expect(gitWorktreeRoot(mainRepo)).toBe(real(mainRepo));
+    expect(gitWorktreeRoot(nonGit)).toBeNull();
+  });
+
+  it('warning names both trees and the fix', () => {
+    const msg = worktreeMismatchWarning(detectWorktreeIndexMismatch(worktree, mainRepo)!);
+    expect(msg).toContain(real(worktree));
+    expect(msg).toContain(real(mainRepo));
+    expect(msg).toContain('codegraph init');
+  });
+});
diff --git a/src/bin/codegraph.ts b/src/bin/codegraph.ts
index dac8ce1e..04c4e08f 100644
--- a/src/bin/codegraph.ts
+++ b/src/bin/codegraph.ts
@@ -22,6 +22,7 @@ import { Command } from 'commander';
 import * as path from 'path';
 import * as fs from 'fs';
 import { getCodeGraphDir, isInitialized } from '../directory';
+import { detectWorktreeIndexMismatch, worktreeMismatchWarning } from '../sync/worktree';
 import { createShimmerProgress } from '../ui/shimmer-progress';
 import { getGlyphs } from '../ui/glyphs';
 
@@ -680,6 +681,11 @@ program
   .option('-j, --json', 'Output as JSON')
   .action(async (pathArg: string | undefined, options: { json?: boolean }) => {
     const projectPath = resolveProjectPath(pathArg);
+    // The directory the user actually ran from, before walking up to the index
+    // root. Used to detect when the resolved index lives in a different git
+    // working tree (e.g. a nested worktree borrowing the main checkout's index).
+    const startPath = path.resolve(pathArg || process.cwd());
+    const worktreeMismatch = detectWorktreeIndexMismatch(startPath, projectPath);
 
     try {
       if (!isInitialized(projectPath)) {
@@ -719,6 +725,9 @@ program
             modified: changes.modified.length,
             removed: changes.removed.length,
           },
+          worktreeMismatch: worktreeMismatch
+            ? { worktreeRoot: worktreeMismatch.worktreeRoot, indexRoot: worktreeMismatch.indexRoot }
+            : null,
         }));
         cg.destroy();
         return;
@@ -728,6 +737,9 @@ program
 
       // Project info
       console.log(chalk.cyan('Project:'), projectPath);
+      if (worktreeMismatch) {
+        warn(worktreeMismatchWarning(worktreeMismatch));
+      }
       console.log();
 
       // Index stats
diff --git a/src/mcp/tools.ts b/src/mcp/tools.ts
index 3ceb8551..763d5a6f 100644
--- a/src/mcp/tools.ts
+++ b/src/mcp/tools.ts
@@ -5,6 +5,7 @@
  */
 
 import CodeGraph, { findNearestCodeGraphRoot } from '../index';
+import { detectWorktreeIndexMismatch, worktreeMismatchWarning } from '../sync/worktree';
 import type { Node, Edge, SearchResult, Subgraph, TaskContext, NodeKind } from '../types';
 import { createHash } from 'crypto';
 import {
@@ -1351,14 +1352,26 @@ export class ToolHandler {
     const cg = this.getCodeGraph(args.projectPath as string | undefined);
     const stats = cg.getStats();
 
+    // Warn when this index actually belongs to a different git working tree
+    // (e.g. the server resolved up from a nested worktree to the main checkout).
+    // Queries then reflect that tree's branch, not the worktree being edited.
+    const startPath =
+      (args.projectPath as string | undefined) ?? this.defaultProjectHint ?? process.cwd();
+    const mismatch = detectWorktreeIndexMismatch(startPath, cg.getProjectRoot());
+
     const lines: string[] = [
       '## CodeGraph Status',
       '',
+    ];
+    if (mismatch) {
+      lines.push(`> ⚠ ${worktreeMismatchWarning(mismatch).replace(/\n/g, '\n> ')}`, '');
+    }
+    lines.push(
       `**Files indexed:** ${stats.fileCount}`,
       `**Total nodes:** ${stats.nodeCount}`,
       `**Total edges:** ${stats.edgeCount}`,
       `**Database size:** ${(stats.dbSizeBytes / 1024 / 1024).toFixed(2)} MB`,
-    ];
+    );
 
     // Surface the active SQLite backend (node:sqlite, Node's built-in real
     // SQLite — full WAL + FTS5, no native build).
diff --git a/src/sync/index.ts b/src/sync/index.ts
index 1857c5a4..bdd8cdf8 100644
--- a/src/sync/index.ts
+++ b/src/sync/index.ts
@@ -8,6 +8,7 @@
  * - FileWatcher: Debounced fs.watch that auto-triggers sync on file changes
  * - Watch policy: decides when the watcher must be disabled (e.g. WSL2 /mnt)
  * - Git sync hooks: opt-in commit/merge/checkout hooks when watching is off
+ * - Git worktree awareness: detect when a query borrows another tree's index
  * - Content hashing for change detection (in extraction module)
  * - Incremental reindexing (in extraction module)
  */
@@ -23,3 +24,9 @@ export {
   type GitHookName,
   type GitHookResult,
 } from './git-hooks';
+export {
+  gitWorktreeRoot,
+  detectWorktreeIndexMismatch,
+  worktreeMismatchWarning,
+  type WorktreeIndexMismatch,
+} from './worktree';
diff --git a/src/sync/worktree.ts b/src/sync/worktree.ts
new file mode 100644
index 00000000..94cea7e4
--- /dev/null
+++ b/src/sync/worktree.ts
@@ -0,0 +1,100 @@
+/**
+ * Git Worktree Awareness
+ *
+ * A CodeGraph index lives in a `.codegraph/` directory and is resolved by
+ * walking up parent directories to the nearest one (see
+ * `findNearestCodeGraphRoot`). That walk is unaware of git worktrees: when a
+ * worktree is created *inside* the main checkout (e.g. some tools place them
+ * under `.gitignore`d paths like `.claude/worktrees/<name>/`), a command run
+ * from the worktree walks up and silently resolves the MAIN checkout's index.
+ *
+ * Every query then returns results from the main tree's code — usually a
+ * different branch — rather than the worktree the user is actually editing.
+ * Symbols added or changed only in the worktree are invisible. This module
+ * detects that "borrowed index" situation so callers can warn about it.
+ *
+ * Detection is best-effort: when git is unavailable or the path isn't a repo,
+ * it reports "no mismatch" and callers carry on unchanged.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import { execFileSync } from 'child_process';
+
+/**
+ * Absolute, symlink-resolved toplevel of the git working tree that `dir`
+ * belongs to, or null when `dir` isn't inside a git repo (or git is missing).
+ *
+ * `git rev-parse --show-toplevel` returns the per-worktree root: the main
+ * checkout and each linked worktree report their own distinct directory, which
+ * is exactly the distinction this module relies on.
+ */
+export function gitWorktreeRoot(dir: string): string | null {
+  try {
+    const out = execFileSync('git', ['rev-parse', '--show-toplevel'], {
+      cwd: dir,
+      encoding: 'utf8',
+      stdio: ['ignore', 'pipe', 'ignore'],
+    }).trim();
+    return out ? realpath(out) : null;
+  } catch {
+    return null;
+  }
+}
+
+export interface WorktreeIndexMismatch {
+  /** The git working tree the command was run from. */
+  worktreeRoot: string;
+  /** The (different) working tree whose `.codegraph` index is being used. */
+  indexRoot: string;
+}
+
+/**
+ * Detect when `startPath` lives in one git working tree but the resolved
+ * CodeGraph index (`indexRoot`) belongs to a *different* working tree.
+ *
+ * Returns null — meaning "nothing to warn about" — when:
+ *   - `startPath` isn't in a git repo (or git is unavailable),
+ *   - the index already lives in `startPath`'s own working tree, or
+ *   - `indexRoot` isn't itself a working-tree root (an unrelated parent dir
+ *     that merely happens to contain a `.codegraph/`), which keeps non-git
+ *     and monorepo-subdir layouts from producing false warnings.
+ */
+export function detectWorktreeIndexMismatch(
+  startPath: string,
+  indexRoot: string,
+): WorktreeIndexMismatch | null {
+  const worktreeRoot = gitWorktreeRoot(startPath);
+  if (!worktreeRoot) return null;
+
+  const resolvedIndexRoot = realpath(indexRoot);
+  if (worktreeRoot === resolvedIndexRoot) return null;
+
+  // Only flag it when the index root is itself a real working-tree root. This
+  // distinguishes "borrowed another worktree's index" from "index sits in a
+  // plain ancestor directory", and avoids warning outside git entirely.
+  if (gitWorktreeRoot(resolvedIndexRoot) !== resolvedIndexRoot) return null;
+
+  return { worktreeRoot, indexRoot: resolvedIndexRoot };
+}
+
+/** One-line-per-fact warning describing a detected mismatch. */
+export function worktreeMismatchWarning(m: WorktreeIndexMismatch): string {
+  return (
+    `This CodeGraph index belongs to a different git working tree.\n` +
+    `  Running in: ${m.worktreeRoot}\n` +
+    `  Index from: ${m.indexRoot}\n` +
+    `Results reflect that tree's code (often a different branch), not this worktree — ` +
+    `symbols changed only here are missing. Run "codegraph init -i" in this worktree ` +
+    `for a worktree-local index.`
+  );
+}
+
+/** Resolve symlinks where possible so tmp/realpath quirks don't break equality. */
+function realpath(p: string): string {
+  try {
+    return fs.realpathSync(path.resolve(p));
+  } catch {
+    return path.resolve(p);
+  }
+}