diff --git a/bio2zarr/vcf2zarr/vcz.py b/bio2zarr/vcf2zarr/vcz.py
index 4a502fa..f17487c 100644
--- a/bio2zarr/vcf2zarr/vcz.py
+++ b/bio2zarr/vcf2zarr/vcz.py
@@ -950,6 +950,7 @@ def create_index(self):
             shape=index.shape,
             dtype=index.dtype,
             compressor=numcodecs.Blosc("zstd", clevel=9, shuffle=0),
+            dimension_separator=self.metadata.dimension_separator,
         )
         array.attrs["_ARRAY_DIMENSIONS"] = [
             "region_index_values",