diff --git a/pre_commit/commands/autoupdate.py b/pre_commit/commands/autoupdate.py
index 27b8d98d..293c81fc 100644
--- a/pre_commit/commands/autoupdate.py
+++ b/pre_commit/commands/autoupdate.py
@@ -54,7 +54,7 @@ def _update_repo(repo_config, runner, tags_only):
     new_repo = Repository.create(new_config, runner.store)
 
     # See if any of our hooks were deleted with the new commits
-    hooks = {hook_id for hook_id, _ in repo.hooks}
+    hooks = {hook['id'] for hook in repo.repo_config['hooks']}
     hooks_missing = hooks - (hooks & set(new_repo.manifest.hooks))
     if hooks_missing:
         raise RepositoryCannotBeUpdatedError(
diff --git a/pre_commit/manifest.py b/pre_commit/manifest.py
index 8827eccc..55f7c1ae 100644
--- a/pre_commit/manifest.py
+++ b/pre_commit/manifest.py
@@ -22,9 +22,7 @@ class Manifest(object):
         repo_path = self.repo_path_getter.repo_path
         default_path = os.path.join(repo_path, C.MANIFEST_FILE)
         legacy_path = os.path.join(repo_path, C.MANIFEST_FILE_LEGACY)
-        if os.path.exists(default_path):
-            return load_manifest(default_path)
-        else:
+        if os.path.exists(legacy_path) and not os.path.exists(default_path):
             logger.warning(
                 '{} uses legacy {} to provide hooks.\n'
                 'In newer versions, this file is called {}\n'
@@ -36,6 +34,8 @@ class Manifest(object):
                 )
             )
             return load_manifest(legacy_path)
+        else:
+            return load_manifest(default_path)
 
     @cached_property
     def hooks(self):
diff --git a/tests/commands/autoupdate_test.py b/tests/commands/autoupdate_test.py
index 29bc087b..b5858ff0 100644
--- a/tests/commands/autoupdate_test.py
+++ b/tests/commands/autoupdate_test.py
@@ -51,6 +51,35 @@ def test_autoupdate_up_to_date_repo(
     assert before == after
 
 
+def test_autoupdate_old_revision_broken(
+    tempdir_factory, in_tmpdir, mock_out_store_directory,
+):
+    """In $FUTURE_VERSION, hooks.yaml will no longer be supported.  This
+    asserts that when that day comes, pre-commit will be able to autoupdate
+    despite not being able to read hooks.yaml in that repository.
+    """
+    path = make_repo(tempdir_factory, 'python_hooks_repo')
+    config = make_config_from_repo(path, check=False)
+
+    with cwd(path):
+        cmd_output('git', 'mv', C.MANIFEST_FILE, 'nope.yaml')
+        cmd_output('git', 'commit', '-m', 'simulate old repo')
+        # Assume this is the revision the user's old repository was at
+        rev = get_head_sha(path)
+        cmd_output('git', 'mv', 'nope.yaml', C.MANIFEST_FILE)
+        cmd_output('git', 'commit', '-m', 'move hooks file')
+        update_rev = get_head_sha(path)
+
+    config['sha'] = rev
+    write_config('.', config)
+    before = open(C.CONFIG_FILE).read()
+    ret = autoupdate(Runner('.', C.CONFIG_FILE), tags_only=False)
+    after = open(C.CONFIG_FILE).read()
+    assert ret == 0
+    assert before != after
+    assert update_rev in after
+
+
 @pytest.yield_fixture
 def out_of_date_repo(tempdir_factory):
     path = make_repo(tempdir_factory, 'python_hooks_repo')