diff --git a/usr.sbin/mergemaster/mergemaster.sh b/usr.sbin/mergemaster/mergemaster.sh
index c5ed5fdfa26f..a200088b1194 100755
--- a/usr.sbin/mergemaster/mergemaster.sh
+++ b/usr.sbin/mergemaster/mergemaster.sh
@@ -709,7 +709,7 @@ case "${RERUN}" in
   # and to make the actual comparison faster.
   find ${TEMPROOT}/usr -type l -delete 2>/dev/null
   find ${TEMPROOT} -type f -size 0 -delete 2>/dev/null
-  find -d ${TEMPROOT} -type d -empty -delete 2>/dev/null
+  find -d ${TEMPROOT} -type d -empty -mindepth 1 -delete 2>/dev/null
 
   # Build the mtree database in a temporary location.
   case "${PRE_WORLD}" in