diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index 4ec734b..3dd54ab 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -60,7 +60,7 @@ for entry in "${GENOMES[@]}"; do
 
         cd "${WORK_DIR}/${MASTER_REPO}"
         git add .gitmodules "${GENOME_NAME}"
-        git commit -m "chore: register submodule ${GENOME_NAME}"
+        git diff --cached --quiet || git commit -m "chore: register submodule ${GENOME_NAME}"
         git push
 
         # Commit the submodule reference in the master repo