diff --git a/flit/vcs/__init__.py b/flit/vcs/__init__.py
index a3e92b39..fe364e52 100644
--- a/flit/vcs/__init__.py
+++ b/flit/vcs/__init__.py
@@ -1,3 +1,4 @@
+import subprocess
 from pathlib import Path
 
 from . import hg
@@ -7,7 +8,14 @@ def identify_vcs(directory: Path):
     directory = directory.resolve()
     for p in [directory] + list(directory.parents):
         if (p / '.git').is_dir():
-            return git
+            check_ignore = subprocess.run(
+                ['git', 'check-ignore', '.'],
+                cwd=str(directory),
+                stderr=subprocess.DEVNULL,
+                stdout=subprocess.DEVNULL,
+            ).returncode
+            if check_ignore != 0:
+                return git
         if (p / '.hg').is_dir():
             return hg