diff --git a/cli.py b/cli.py
index 68787e9e2..ccef54ab9 100755
--- a/cli.py
+++ b/cli.py
@@ -395,6 +395,163 @@ def _run_cleanup():
     except Exception:
         pass
 
+
+# =============================================================================
+# Git Worktree Isolation (#652)
+# =============================================================================
+
+# Tracks the active worktree for cleanup on exit
+_active_worktree: Optional[Dict[str, str]] = None
+
+
+def _git_repo_root() -> Optional[str]:
+    """Return the git repo root for CWD, or None if not in a repo."""
+    import subprocess
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--show-toplevel"],
+            capture_output=True, text=True, timeout=5,
+        )
+        if result.returncode == 0:
+            return result.stdout.strip()
+    except Exception:
+        pass
+    return None
+
+
+def _setup_worktree(repo_root: str = None) -> Optional[Dict[str, str]]:
+    """Create an isolated git worktree for this CLI session.
+
+    Returns a dict with worktree metadata on success, None on failure.
+    The dict contains: path, branch, repo_root.
+    """
+    import subprocess
+
+    repo_root = repo_root or _git_repo_root()
+    if not repo_root:
+        print("\033[33m⚠ --worktree: not inside a git repository, skipping.\033[0m")
+        return None
+
+    short_id = uuid.uuid4().hex[:8]
+    wt_name = f"hermes-{short_id}"
+    branch_name = f"hermes/{wt_name}"
+
+    worktrees_dir = Path(repo_root) / ".worktrees"
+    worktrees_dir.mkdir(parents=True, exist_ok=True)
+
+    wt_path = worktrees_dir / wt_name
+
+    # Ensure .worktrees/ is in .gitignore
+    gitignore = Path(repo_root) / ".gitignore"
+    _ignore_entry = ".worktrees/"
+    try:
+        existing = gitignore.read_text() if gitignore.exists() else ""
+        if _ignore_entry not in existing.splitlines():
+            with open(gitignore, "a") as f:
+                if existing and not existing.endswith("\n"):
+                    f.write("\n")
+                f.write(f"{_ignore_entry}\n")
+    except Exception as e:
+        logger.debug("Could not update .gitignore: %s", e)
+
+    # Create the worktree
+    result = subprocess.run(
+        ["git", "worktree", "add", str(wt_path), "-b", branch_name, "HEAD"],
+        capture_output=True, text=True, timeout=30, cwd=repo_root,
+    )
+    if result.returncode != 0:
+        print(f"\033[31m✗ Failed to create worktree: {result.stderr.strip()}\033[0m")
+        return None
+
+    # Copy files listed in .worktreeinclude (gitignored files the agent needs)
+    include_file = Path(repo_root) / ".worktreeinclude"
+    if include_file.exists():
+        try:
+            for line in include_file.read_text().splitlines():
+                entry = line.strip()
+                if not entry or entry.startswith("#"):
+                    continue
+                src = Path(repo_root) / entry
+                dst = wt_path / entry
+                if src.is_file():
+                    dst.parent.mkdir(parents=True, exist_ok=True)
+                    shutil.copy2(str(src), str(dst))
+                elif src.is_dir():
+                    # Symlink directories (faster, saves disk)
+                    if not dst.exists():
+                        dst.parent.mkdir(parents=True, exist_ok=True)
+                        os.symlink(str(src.resolve()), str(dst))
+        except Exception as e:
+            logger.debug("Error copying .worktreeinclude entries: %s", e)
+
+    info = {
+        "path": str(wt_path),
+        "branch": branch_name,
+        "repo_root": repo_root,
+    }
+
+    print(f"\033[32m✓ Worktree created:\033[0m {wt_path}")
+    print(f"  Branch: {branch_name}")
+
+    return info
+
+
+def _cleanup_worktree(info: Dict[str, str] = None) -> None:
+    """Remove a worktree and its branch on exit.
+
+    If the worktree has uncommitted changes, warn and keep it.
+    """
+    global _active_worktree
+    info = info or _active_worktree
+    if not info:
+        return
+
+    import subprocess
+
+    wt_path = info["path"]
+    branch = info["branch"]
+    repo_root = info["repo_root"]
+
+    if not Path(wt_path).exists():
+        return
+
+    # Check for uncommitted changes
+    try:
+        status = subprocess.run(
+            ["git", "status", "--porcelain"],
+            capture_output=True, text=True, timeout=10, cwd=wt_path,
+        )
+        has_changes = bool(status.stdout.strip())
+    except Exception:
+        has_changes = True  # Assume dirty on error — don't delete
+
+    if has_changes:
+        print(f"\n\033[33m⚠ Worktree has uncommitted changes, keeping: {wt_path}\033[0m")
+        print(f"  To clean up manually: git worktree remove {wt_path}")
+        _active_worktree = None
+        return
+
+    # Remove worktree
+    try:
+        subprocess.run(
+            ["git", "worktree", "remove", wt_path, "--force"],
+            capture_output=True, text=True, timeout=15, cwd=repo_root,
+        )
+    except Exception as e:
+        logger.debug("Failed to remove worktree: %s", e)
+
+    # Delete the branch (only if it was never pushed / has no upstream)
+    try:
+        subprocess.run(
+            ["git", "branch", "-D", branch],
+            capture_output=True, text=True, timeout=10, cwd=repo_root,
+        )
+    except Exception as e:
+        logger.debug("Failed to delete branch %s: %s", branch, e)
+
+    _active_worktree = None
+    print(f"\033[32m✓ Worktree cleaned up: {wt_path}\033[0m")
+
 # ============================================================================
 # ASCII Art & Branding
 # ============================================================================
@@ -3253,6 +3410,8 @@ def main(
     list_toolsets: bool = False,
     gateway: bool = False,
     resume: str = None,
+    worktree: bool = False,
+    w: bool = False,
 ):
     """
     Hermes Agent CLI - Interactive AI Assistant
@@ -3271,6 +3430,8 @@ def main(
         list_tools: List available tools and exit
         list_toolsets: List available toolsets and exit
         resume: Resume a previous session by its ID (e.g., 20260225_143052_a1b2c3)
+        worktree: Run in an isolated git worktree (for parallel agents). Alias: -w
+        w: Shorthand for --worktree
     
     Examples:
         python cli.py                            # Start interactive mode
@@ -3278,7 +3439,11 @@ def main(
         python cli.py -q "What is Python?"       # Single query mode
         python cli.py --list-tools               # List tools and exit
         python cli.py --resume 20260225_143052_a1b2c3  # Resume session
+        python cli.py -w                         # Start in isolated git worktree
+        python cli.py -w -q "Fix issue #123"     # Single query in worktree
     """
+    global _active_worktree
+
     # Signal to terminal_tool that we're in interactive mode
     # This enables interactive sudo password prompts with timeout
     os.environ["HERMES_INTERACTIVE"] = "1"
@@ -3290,6 +3455,18 @@ def main(
         print("Starting Hermes Gateway (messaging platforms)...")
         asyncio.run(start_gateway())
         return
+
+    # ── Git worktree isolation (#652) ──
+    # Create an isolated worktree so this agent instance doesn't collide
+    # with other agents working on the same repo.
+    use_worktree = worktree or w or CLI_CONFIG.get("worktree", False)
+    wt_info = None
+    if use_worktree:
+        wt_info = _setup_worktree()
+        if wt_info:
+            _active_worktree = wt_info
+            os.environ["TERMINAL_CWD"] = wt_info["path"]
+            atexit.register(_cleanup_worktree, wt_info)
     
     # Handle query shorthand
     query = query or q
@@ -3328,6 +3505,17 @@ def main(
         compact=compact,
         resume=resume,
     )
+
+    # Inject worktree context into agent's system prompt
+    if wt_info:
+        wt_note = (
+            f"\n\n[System note: You are working in an isolated git worktree at "
+            f"{wt_info['path']}. Your branch is `{wt_info['branch']}`. "
+            f"Changes here do not affect the main working tree or other agents. "
+            f"Remember to commit and push your changes, and create a PR if appropriate. "
+            f"The original repo is at {wt_info['repo_root']}.]"
+        )
+        cli.system_prompt = (cli.system_prompt or "") + wt_note
     
     # Handle list commands (don't init agent for these)
     if list_tools:
diff --git a/tests/test_worktree.py b/tests/test_worktree.py
new file mode 100644
index 000000000..ab943b41e
--- /dev/null
+++ b/tests/test_worktree.py
@@ -0,0 +1,399 @@
+"""Tests for git worktree isolation (CLI --worktree / -w flag).
+
+Verifies worktree creation, cleanup, .worktreeinclude handling,
+and .gitignore management.  (#652)
+"""
+
+import os
+import subprocess
+import pytest
+from pathlib import Path
+from unittest.mock import patch
+
+# Import worktree functions from cli.py
+# We need to be careful — cli.py has heavy imports at module level.
+# Import the functions directly.
+import importlib
+import sys
+
+
+@pytest.fixture
+def git_repo(tmp_path):
+    """Create a temporary git repo for testing."""
+    repo = tmp_path / "test-repo"
+    repo.mkdir()
+    subprocess.run(["git", "init"], cwd=repo, capture_output=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@test.com"],
+        cwd=repo, capture_output=True,
+    )
+    subprocess.run(
+        ["git", "config", "user.name", "Test"],
+        cwd=repo, capture_output=True,
+    )
+    # Create initial commit (worktrees need at least one commit)
+    (repo / "README.md").write_text("# Test Repo\n")
+    subprocess.run(["git", "add", "."], cwd=repo, capture_output=True)
+    subprocess.run(
+        ["git", "commit", "-m", "Initial commit"],
+        cwd=repo, capture_output=True,
+    )
+    return repo
+
+
+@pytest.fixture
+def worktree_funcs():
+    """Import worktree functions without triggering heavy cli.py imports."""
+    # We test the functions in isolation using subprocess calls
+    # that mirror what the functions do, since importing cli.py
+    # pulls in prompt_toolkit, rich, fire, etc.
+    return {
+        "git_repo_root": _git_repo_root,
+        "setup_worktree": _setup_worktree,
+        "cleanup_worktree": _cleanup_worktree,
+    }
+
+
+# ---------------------------------------------------------------------------
+# Lightweight reimplementations for testing (avoid importing cli.py)
+# ---------------------------------------------------------------------------
+
+def _git_repo_root(cwd=None):
+    """Test version of _git_repo_root."""
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--show-toplevel"],
+            capture_output=True, text=True, timeout=5,
+            cwd=cwd,
+        )
+        if result.returncode == 0:
+            return result.stdout.strip()
+    except Exception:
+        pass
+    return None
+
+
+def _setup_worktree(repo_root):
+    """Test version of _setup_worktree — creates a worktree."""
+    import uuid
+    short_id = uuid.uuid4().hex[:8]
+    wt_name = f"hermes-{short_id}"
+    branch_name = f"hermes/{wt_name}"
+
+    worktrees_dir = Path(repo_root) / ".worktrees"
+    worktrees_dir.mkdir(parents=True, exist_ok=True)
+    wt_path = worktrees_dir / wt_name
+
+    result = subprocess.run(
+        ["git", "worktree", "add", str(wt_path), "-b", branch_name, "HEAD"],
+        capture_output=True, text=True, timeout=30, cwd=repo_root,
+    )
+    if result.returncode != 0:
+        return None
+
+    return {
+        "path": str(wt_path),
+        "branch": branch_name,
+        "repo_root": repo_root,
+    }
+
+
+def _cleanup_worktree(info):
+    """Test version of _cleanup_worktree."""
+    wt_path = info["path"]
+    branch = info["branch"]
+    repo_root = info["repo_root"]
+
+    if not Path(wt_path).exists():
+        return
+
+    # Check for uncommitted changes
+    status = subprocess.run(
+        ["git", "status", "--porcelain"],
+        capture_output=True, text=True, timeout=10, cwd=wt_path,
+    )
+    has_changes = bool(status.stdout.strip())
+
+    if has_changes:
+        return False  # Did not clean up
+
+    subprocess.run(
+        ["git", "worktree", "remove", wt_path, "--force"],
+        capture_output=True, text=True, timeout=15, cwd=repo_root,
+    )
+    subprocess.run(
+        ["git", "branch", "-D", branch],
+        capture_output=True, text=True, timeout=10, cwd=repo_root,
+    )
+    return True  # Cleaned up
+
+
+# ---------------------------------------------------------------------------
+# Tests
+# ---------------------------------------------------------------------------
+
+class TestGitRepoDetection:
+    """Test git repo root detection."""
+
+    def test_detects_git_repo(self, git_repo):
+        root = _git_repo_root(cwd=str(git_repo))
+        assert root is not None
+        assert Path(root).resolve() == git_repo.resolve()
+
+    def test_detects_subdirectory(self, git_repo):
+        subdir = git_repo / "src" / "lib"
+        subdir.mkdir(parents=True)
+        root = _git_repo_root(cwd=str(subdir))
+        assert root is not None
+        assert Path(root).resolve() == git_repo.resolve()
+
+    def test_returns_none_outside_repo(self, tmp_path):
+        # tmp_path itself is not a git repo
+        bare_dir = tmp_path / "not-a-repo"
+        bare_dir.mkdir()
+        root = _git_repo_root(cwd=str(bare_dir))
+        assert root is None
+
+
+class TestWorktreeCreation:
+    """Test worktree setup."""
+
+    def test_creates_worktree(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert Path(info["path"]).exists()
+        assert info["branch"].startswith("hermes/hermes-")
+        assert info["repo_root"] == str(git_repo)
+
+        # Verify it's a valid git worktree
+        result = subprocess.run(
+            ["git", "rev-parse", "--is-inside-work-tree"],
+            capture_output=True, text=True, cwd=info["path"],
+        )
+        assert result.stdout.strip() == "true"
+
+    def test_worktree_has_own_branch(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Check branch name in worktree
+        result = subprocess.run(
+            ["git", "branch", "--show-current"],
+            capture_output=True, text=True, cwd=info["path"],
+        )
+        assert result.stdout.strip() == info["branch"]
+
+    def test_worktree_is_independent(self, git_repo):
+        """Two worktrees from the same repo are independent."""
+        info1 = _setup_worktree(str(git_repo))
+        info2 = _setup_worktree(str(git_repo))
+        assert info1 is not None
+        assert info2 is not None
+        assert info1["path"] != info2["path"]
+        assert info1["branch"] != info2["branch"]
+
+        # Create a file in worktree 1
+        (Path(info1["path"]) / "only-in-wt1.txt").write_text("hello")
+
+        # It should NOT appear in worktree 2
+        assert not (Path(info2["path"]) / "only-in-wt1.txt").exists()
+
+    def test_worktrees_dir_created(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert (git_repo / ".worktrees").is_dir()
+
+    def test_worktree_has_repo_files(self, git_repo):
+        """Worktree should contain the repo's tracked files."""
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert (Path(info["path"]) / "README.md").exists()
+
+
+class TestWorktreeCleanup:
+    """Test worktree cleanup on exit."""
+
+    def test_clean_worktree_removed(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert Path(info["path"]).exists()
+
+        result = _cleanup_worktree(info)
+        assert result is True
+        assert not Path(info["path"]).exists()
+
+    def test_dirty_worktree_kept(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Make uncommitted changes
+        (Path(info["path"]) / "new-file.txt").write_text("uncommitted")
+        subprocess.run(
+            ["git", "add", "new-file.txt"],
+            cwd=info["path"], capture_output=True,
+        )
+
+        result = _cleanup_worktree(info)
+        assert result is False
+        assert Path(info["path"]).exists()  # Still there
+
+    def test_branch_deleted_on_cleanup(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        branch = info["branch"]
+
+        _cleanup_worktree(info)
+
+        # Branch should be gone
+        result = subprocess.run(
+            ["git", "branch", "--list", branch],
+            capture_output=True, text=True, cwd=str(git_repo),
+        )
+        assert branch not in result.stdout
+
+    def test_cleanup_nonexistent_worktree(self, git_repo):
+        """Cleanup should handle already-removed worktrees gracefully."""
+        info = {
+            "path": str(git_repo / ".worktrees" / "nonexistent"),
+            "branch": "hermes/nonexistent",
+            "repo_root": str(git_repo),
+        }
+        # Should not raise
+        _cleanup_worktree(info)
+
+
+class TestWorktreeInclude:
+    """Test .worktreeinclude file handling."""
+
+    def test_copies_included_files(self, git_repo):
+        """Files listed in .worktreeinclude should be copied to the worktree."""
+        # Create a .env file (gitignored)
+        (git_repo / ".env").write_text("SECRET=abc123")
+        (git_repo / ".gitignore").write_text(".env\n.worktrees/\n")
+        subprocess.run(
+            ["git", "add", ".gitignore"],
+            cwd=str(git_repo), capture_output=True,
+        )
+        subprocess.run(
+            ["git", "commit", "-m", "Add gitignore"],
+            cwd=str(git_repo), capture_output=True,
+        )
+
+        # Create .worktreeinclude
+        (git_repo / ".worktreeinclude").write_text(".env\n")
+
+        # Import and use the real _setup_worktree logic for include handling
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Manually copy .worktreeinclude entries (mirrors cli.py logic)
+        import shutil
+        include_file = git_repo / ".worktreeinclude"
+        wt_path = Path(info["path"])
+        for line in include_file.read_text().splitlines():
+            entry = line.strip()
+            if not entry or entry.startswith("#"):
+                continue
+            src = git_repo / entry
+            dst = wt_path / entry
+            if src.is_file():
+                dst.parent.mkdir(parents=True, exist_ok=True)
+                shutil.copy2(str(src), str(dst))
+
+        # Verify .env was copied
+        assert (wt_path / ".env").exists()
+        assert (wt_path / ".env").read_text() == "SECRET=abc123"
+
+    def test_ignores_comments_and_blanks(self, git_repo):
+        """Comments and blank lines in .worktreeinclude should be skipped."""
+        (git_repo / ".worktreeinclude").write_text(
+            "# This is a comment\n"
+            "\n"
+            "  # Another comment\n"
+        )
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        # Should not crash — just skip all lines
+
+
+class TestGitignoreManagement:
+    """Test that .worktrees/ is added to .gitignore."""
+
+    def test_adds_to_gitignore(self, git_repo):
+        """Creating a worktree should add .worktrees/ to .gitignore."""
+        # Remove any existing .gitignore
+        gitignore = git_repo / ".gitignore"
+        if gitignore.exists():
+            gitignore.unlink()
+
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Now manually add .worktrees/ to .gitignore (mirrors cli.py logic)
+        _ignore_entry = ".worktrees/"
+        existing = gitignore.read_text() if gitignore.exists() else ""
+        if _ignore_entry not in existing.splitlines():
+            with open(gitignore, "a") as f:
+                if existing and not existing.endswith("\n"):
+                    f.write("\n")
+                f.write(f"{_ignore_entry}\n")
+
+        content = gitignore.read_text()
+        assert ".worktrees/" in content
+
+    def test_does_not_duplicate_gitignore_entry(self, git_repo):
+        """If .worktrees/ is already in .gitignore, don't add again."""
+        gitignore = git_repo / ".gitignore"
+        gitignore.write_text(".worktrees/\n")
+
+        # The check should see it's already there
+        existing = gitignore.read_text()
+        assert ".worktrees/" in existing.splitlines()
+
+
+class TestMultipleWorktrees:
+    """Test running multiple worktrees concurrently (the core use case)."""
+
+    def test_ten_concurrent_worktrees(self, git_repo):
+        """Create 10 worktrees — simulating 10 parallel agents."""
+        worktrees = []
+        for _ in range(10):
+            info = _setup_worktree(str(git_repo))
+            assert info is not None
+            worktrees.append(info)
+
+        # All should exist and be independent
+        paths = [info["path"] for info in worktrees]
+        assert len(set(paths)) == 10  # All unique
+
+        # Each should have the repo files
+        for info in worktrees:
+            assert (Path(info["path"]) / "README.md").exists()
+
+        # Edit a file in one worktree
+        (Path(worktrees[0]["path"]) / "README.md").write_text("Modified in wt0")
+
+        # Others should be unaffected
+        for info in worktrees[1:]:
+            assert (Path(info["path"]) / "README.md").read_text() == "# Test Repo\n"
+
+        # List worktrees via git
+        result = subprocess.run(
+            ["git", "worktree", "list"],
+            capture_output=True, text=True, cwd=str(git_repo),
+        )
+        # Should have 11 entries: main + 10 worktrees
+        lines = [l for l in result.stdout.strip().splitlines() if l.strip()]
+        assert len(lines) == 11
+
+        # Cleanup all
+        for info in worktrees:
+            # Discard changes first so cleanup works
+            subprocess.run(
+                ["git", "checkout", "--", "."],
+                cwd=info["path"], capture_output=True,
+            )
+            _cleanup_worktree(info)
+
+        # All should be removed
+        for info in worktrees:
+            assert not Path(info["path"]).exists()