diff --git a/marimo/_cli/pair/commands.py b/marimo/_cli/pair/commands.py
index 59f84b0aaa0..95f9ef2531e 100644
--- a/marimo/_cli/pair/commands.py
+++ b/marimo/_cli/pair/commands.py
@@ -38,13 +38,32 @@ def has_skill(self) -> bool:
         )
 
 
+def _claude_project_roots() -> list[Path]:
+    """Return the `.claude` directories that apply to the current project.
+
+    Claude Code loads project skills from `.claude/skills` in the directory it
+    was started in *and in every parent up to the repository root*, so a skill
+    installed once at the root is available from any subdirectory. Mirror that
+    walk here; checking only the current directory reports the skill missing
+    whenever the notebook lives below the root. Outside a repository there is
+    no root to walk to, so only the current directory applies.
+    """
+    cwd = Path.cwd()
+    candidates = [cwd, *cwd.parents]
+    for index, directory in enumerate(candidates):
+        # A worktree or submodule has `.git` as a file, not a directory.
+        if (directory / ".git").exists():
+            return [d / ".claude" for d in candidates[: index + 1]]
+    return [cwd / ".claude"]
+
+
 def _claude_skill_dirs() -> list[Path]:
     """Return all directories where a Claude Code skill may be installed.
 
     Skills can be installed directly or bundled in a marketplace plugin in
-    both the global (`~/.claude`) and local (`.claude`) config directories.
+    both the global (`~/.claude`) and project (`.claude`) config directories.
     """
-    roots = [Path.home() / ".claude", Path.cwd() / ".claude"]
+    roots = [Path.home() / ".claude", *_claude_project_roots()]
     subdirs = ["skills", "plugins", str(Path("plugins") / "marketplaces")]
     return [
         *[root / sub for root in roots for sub in subdirs],
diff --git a/tests/_cli/test_cli_pair.py b/tests/_cli/test_cli_pair.py
index e5354c9f057..c772fc77548 100644
--- a/tests/_cli/test_cli_pair.py
+++ b/tests/_cli/test_cli_pair.py
@@ -4,18 +4,26 @@
 import hashlib
 import sys
 from pathlib import Path
+from typing import TYPE_CHECKING
 from unittest.mock import patch
 
 from click.testing import CliRunner
 
 from marimo._cli.cli import main as cli_main
 from marimo._cli.pair.commands import (
+    SKILL_FILE,
+    SKILL_NAME,
     AgentConfig,
+    _claude_project_roots,
+    _claude_skill_dirs,
     _opencode_skill_dirs,
     _plugin_skill_dirs,
     pair_agents,
 )
 
+if TYPE_CHECKING:
+    import pytest
+
 _runner = CliRunner()
 
 TEST_URL = "https://localhost:8000?auth=tok123"
@@ -370,3 +378,71 @@ def test_plugin_cache_layout(self, tmp_path: Path) -> None:
             skill_dirs=_plugin_skill_dirs(tmp_path),
         )
         assert agent.has_skill() is True
+
+
+class TestClaudeProjectRoots:
+    """Claude Code resolves project skills from the start directory up to the
+    repository root, so a skill installed once at the root must be found from
+    any subdirectory below it."""
+
+    def test_walks_up_to_repository_root(
+        self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        (tmp_path / ".git").mkdir()
+        nested = tmp_path / "notebooks" / "analysis"
+        nested.mkdir(parents=True)
+        monkeypatch.chdir(nested)
+
+        assert _claude_project_roots() == [
+            nested / ".claude",
+            tmp_path / "notebooks" / ".claude",
+            tmp_path / ".claude",
+        ]
+
+    def test_skill_at_repository_root_found_from_subdirectory(
+        self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        (tmp_path / ".git").mkdir()
+        skill = tmp_path / ".claude" / "skills" / SKILL_NAME
+        skill.mkdir(parents=True)
+        (skill / SKILL_FILE).write_text("test")
+        nested = tmp_path / "notebooks" / "analysis"
+        nested.mkdir(parents=True)
+        monkeypatch.chdir(nested)
+
+        agent = AgentConfig(
+            name="Claude Code", skill_dirs=_claude_skill_dirs()
+        )
+        assert agent.has_skill() is True
+
+    def test_stops_at_repository_root(
+        self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        repo = tmp_path / "repo"
+        (repo / ".git").mkdir(parents=True)
+        monkeypatch.chdir(repo)
+
+        assert tmp_path / ".claude" not in _claude_project_roots()
+
+    def test_git_file_counts_as_root(
+        self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        # Worktrees and submodules record `.git` as a file.
+        (tmp_path / ".git").write_text("gitdir: /elsewhere\n")
+        nested = tmp_path / "sub"
+        nested.mkdir()
+        monkeypatch.chdir(nested)
+
+        assert _claude_project_roots() == [
+            nested / ".claude",
+            tmp_path / ".claude",
+        ]
+
+    def test_outside_repository_uses_cwd_only(
+        self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        nested = tmp_path / "no_repo_here"
+        nested.mkdir()
+        monkeypatch.chdir(nested)
+
+        assert _claude_project_roots() == [nested / ".claude"]