diff --git a/src/gitup/config.py b/src/gitup/config.py
index c3e6bed..1124cbb 100644
--- a/src/gitup/config.py
+++ b/src/gitup/config.py
@@ -147,7 +147,11 @@ def clean_bookmarks(config_path=None):
     delete = [
         path
         for path in bookmarks
-        if not (os.path.isdir(path) or glob(os.path.expanduser(path)))
+        if not (
+            path.lstrip().startswith("#")
+            or os.path.isdir(path)
+            or glob(os.path.expanduser(path))
+        )
     ]
     if not delete:
         print("All of your bookmarks are valid.")
diff --git a/src/gitup/test/test_bookmarks.py b/src/gitup/test/test_bookmarks.py
index c051432..9f64ac2 100644
--- a/src/gitup/test/test_bookmarks.py
+++ b/src/gitup/test/test_bookmarks.py
@@ -3,6 +3,8 @@
 # Copyright (C) 2011-2018 Ben Kurtovic <ben.kurtovic@gmail.com>
 # Released under the terms of the MIT License. See LICENSE for details.
 
+import os
+
 from gitup import config
 
 
@@ -11,3 +13,27 @@ def test_empty_list(tmpdir, capsys):
     config.list_bookmarks(config_path)
     captured = capsys.readouterr()
     assert captured.out == "You have no bookmarks to display.\n"
+
+
+def test_clean_bookmarks_preserves_comments(tmpdir, capsys):
+    """Comments in the bookmarks file must survive a cleanup."""
+    repo_dir = tmpdir / "repo"
+    os.makedirs(os.fspath(repo_dir))
+    missing_dir = tmpdir / "missing"
+
+    config_path = tmpdir / "config"
+    comment = "# a comment line"
+    lines = [comment, os.fspath(repo_dir), os.fspath(missing_dir)]
+    with open(os.fspath(config_path), "wb") as handle:
+        handle.write("\n".join(lines).encode("utf8"))
+
+    config.clean_bookmarks(config_path)
+
+    remaining = config_path.read_binary().decode("utf8").split("\n")
+    assert comment in remaining
+    assert os.fspath(repo_dir) in remaining
+    assert os.fspath(missing_dir) not in remaining
+
+    captured = capsys.readouterr()
+    assert "Deleted bookmarks:" in captured.out
+    assert os.fspath(missing_dir) in captured.out