diff --git a/builtin/rebase.c b/builtin/rebase.c
index 625f50c637..ee2bc8b032 100644
--- a/builtin/rebase.c
+++ b/builtin/rebase.c
@@ -62,7 +62,7 @@ struct rebase_options {
 	const char *onto_name;
 	const char *revisions;
 	const char *switch_to;
-	int root;
+	int root, root_with_onto;
 	struct object_id *squash_onto;
 	struct commit *restrict_revision;
 	int dont_finish_rebase;
@@ -374,6 +374,7 @@ static int run_rebase_interactive(struct rebase_options *opts,
 	flags |= abbreviate_commands ? TODO_LIST_ABBREVIATE_CMDS : 0;
 	flags |= opts->rebase_merges ? TODO_LIST_REBASE_MERGES : 0;
 	flags |= opts->rebase_cousins > 0 ? TODO_LIST_REBASE_COUSINS : 0;
+	flags |= opts->root_with_onto ? TODO_LIST_ROOT_WITH_ONTO : 0;
 	flags |= command == ACTION_SHORTEN_OIDS ? TODO_LIST_SHORTEN_IDS : 0;
 
 	switch (command) {
@@ -1841,7 +1842,9 @@ int cmd_rebase(int argc, const char **argv, const char *prefix)
 			options.squash_onto = &squash_onto;
 			options.onto_name = squash_onto_name =
 				xstrdup(oid_to_hex(&squash_onto));
-		}
+		} else
+			options.root_with_onto = 1;
+
 		options.upstream_name = NULL;
 		options.upstream = NULL;
 		if (argc > 1)
diff --git a/sequencer.c b/sequencer.c
index d228448cd8..ca119c84e5 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -4440,6 +4440,7 @@ static int make_script_with_merges(struct pretty_print_context *pp,
 {
 	int keep_empty = flags & TODO_LIST_KEEP_EMPTY;
 	int rebase_cousins = flags & TODO_LIST_REBASE_COUSINS;
+	int root_with_onto = flags & TODO_LIST_ROOT_WITH_ONTO;
 	struct strbuf buf = STRBUF_INIT, oneline = STRBUF_INIT;
 	struct strbuf label = STRBUF_INIT;
 	struct commit_list *commits = NULL, **tail = &commits, *iter;
@@ -4606,7 +4607,8 @@ static int make_script_with_merges(struct pretty_print_context *pp,
 
 		if (!commit)
 			strbuf_addf(out, "%s %s\n", cmd_reset,
-				    rebase_cousins ? "onto" : "[new root]");
+				    rebase_cousins || root_with_onto ?
+				    "onto" : "[new root]");
 		else {
 			const char *to = NULL;
 
diff --git a/sequencer.h b/sequencer.h
index 0c494b83d4..d506081d3c 100644
--- a/sequencer.h
+++ b/sequencer.h
@@ -142,6 +142,12 @@ int sequencer_remove_state(struct replay_opts *opts);
  */
 #define TODO_LIST_REBASE_COUSINS (1U << 4)
 #define TODO_LIST_APPEND_TODO_HELP (1U << 5)
+/*
+ * When generating a script that rebases merges with `--root` *and* with
+ * `--onto`, we do not want to re-generate the root commits.
+ */
+#define TODO_LIST_ROOT_WITH_ONTO (1U << 6)
+
 
 int sequencer_make_script(struct repository *r, struct strbuf *out, int argc,
 			  const char **argv, unsigned flags);
diff --git a/t/t3427-rebase-subtree.sh b/t/t3427-rebase-subtree.sh
index 7a37235768..39e348de16 100755
--- a/t/t3427-rebase-subtree.sh
+++ b/t/t3427-rebase-subtree.sh
@@ -93,4 +93,15 @@ test_expect_success 'Rebase -Xsubtree --keep-empty --onto commit' '
 	verbose test "$(commit_message HEAD)" = "Empty commit"
 '
 
+test_expect_success 'Rebase -Xsubtree --keep-empty --rebase-merges --onto commit' '
+	reset_rebase &&
+	git checkout -b rebase-merges-onto to-rebase &&
+	test_must_fail git rebase -Xsubtree=files_subtree --keep-empty --rebase-merges --onto files-master --root &&
+	: first pick results in no changes &&
+	git rebase --continue &&
+	verbose test "$(commit_message HEAD~2)" = "master4" &&
+	verbose test "$(commit_message HEAD~)" = "files_subtree/master5" &&
+	verbose test "$(commit_message HEAD)" = "Empty commit"
+'
+
 test_done