diff --git a/pairtools/cli/dedup.py b/pairtools/cli/dedup.py
index 5ec4f4c..5a2802c 100644
--- a/pairtools/cli/dedup.py
+++ b/pairtools/cli/dedup.py
@@ -140,10 +140,11 @@
 
 ### Output options:
 @click.option(
-    "--mark-dups",
+    "--mark-dups/--no-mark-dups",
+    default=True,
     is_flag=True,
-    help='If specified, duplicate pairs are marked as DD in "pair_type" and '
-    "as a duplicate in the sam entries. [output format option]",
+    help='Specify if duplicate pairs should be marked as DD in "pair_type" and '
+    "as a duplicate in the sam entries. True by default. [output format option]",
 )
 @click.option(
     "--keep-parent-id",