diff --git a/branch.c b/branch.c
index 3364adf182..d013374e5a 100644
--- a/branch.c
+++ b/branch.c
@@ -311,21 +311,23 @@ void remove_branch_state(void)
 	unlink(git_path_squash_msg());
 }
 
-static void check_linked_checkout(const char *branch, const char *id)
+static char *find_linked_symref(const char *symref, const char *branch,
+				const char *id)
 {
 	struct strbuf sb = STRBUF_INIT;
 	struct strbuf path = STRBUF_INIT;
 	struct strbuf gitdir = STRBUF_INIT;
+	char *existing = NULL;
 
 	/*
-	 * $GIT_COMMON_DIR/HEAD is practically outside
-	 * $GIT_DIR so resolve_ref_unsafe() won't work (it
-	 * uses git_path). Parse the ref ourselves.
+	 * $GIT_COMMON_DIR/$symref (e.g. HEAD) is practically outside
+	 * $GIT_DIR so resolve_ref_unsafe() won't work (it uses
+	 * git_path). Parse the ref ourselves.
 	 */
 	if (id)
-		strbuf_addf(&path, "%s/worktrees/%s/HEAD", get_git_common_dir(), id);
+		strbuf_addf(&path, "%s/worktrees/%s/%s", get_git_common_dir(), id, symref);
 	else
-		strbuf_addf(&path, "%s/HEAD", get_git_common_dir());
+		strbuf_addf(&path, "%s/%s", get_git_common_dir(), symref);
 
 	if (!strbuf_readlink(&sb, path.buf, 0)) {
 		if (!starts_with(sb.buf, "refs/") ||
@@ -347,33 +349,53 @@ static void check_linked_checkout(const char *branch, const char *id)
 		strbuf_rtrim(&gitdir);
 	} else
 		strbuf_addstr(&gitdir, get_git_common_dir());
-	skip_prefix(branch, "refs/heads/", &branch);
 	strbuf_strip_suffix(&gitdir, ".git");
-	die(_("'%s' is already checked out at '%s'"), branch, gitdir.buf);
+
+	existing = strbuf_detach(&gitdir, NULL);
 done:
 	strbuf_release(&path);
 	strbuf_release(&sb);
 	strbuf_release(&gitdir);
+
+	return existing;
 }
 
-void die_if_checked_out(const char *branch)
+char *find_shared_symref(const char *symref, const char *target)
 {
 	struct strbuf path = STRBUF_INIT;
 	DIR *dir;
 	struct dirent *d;
+	char *existing;
 
-	check_linked_checkout(branch, NULL);
+	if ((existing = find_linked_symref(symref, target, NULL)))
+		return existing;
 
 	strbuf_addf(&path, "%s/worktrees", get_git_common_dir());
 	dir = opendir(path.buf);
 	strbuf_release(&path);
 	if (!dir)
-		return;
+		return NULL;
 
 	while ((d = readdir(dir)) != NULL) {
 		if (!strcmp(d->d_name, ".") || !strcmp(d->d_name, ".."))
 			continue;
-		check_linked_checkout(branch, d->d_name);
+		existing = find_linked_symref(symref, target, d->d_name);
+		if (existing)
+			goto done;
 	}
+done:
 	closedir(dir);
+
+	return existing;
+}
+
+void die_if_checked_out(const char *branch)
+{
+	char *existing;
+
+	existing = find_shared_symref("HEAD", branch);
+	if (existing) {
+		skip_prefix(branch, "refs/heads/", &branch);
+		die(_("'%s' is already checked out at '%s'"), branch, existing);
+	}
 }
diff --git a/branch.h b/branch.h
index 58aa45fe72..d3446ed73c 100644
--- a/branch.h
+++ b/branch.h
@@ -59,4 +59,12 @@ extern int read_branch_desc(struct strbuf *, const char *branch_name);
  */
 extern void die_if_checked_out(const char *branch);
 
+/*
+ * Check if a per-worktree symref points to a ref in the main worktree
+ * or any linked worktree, and return the path to the exising worktree
+ * if it is.  Returns NULL if there is no existing ref.  The caller is
+ * responsible for freeing the returned path.
+ */
+extern char *find_shared_symref(const char *symref, const char *target);
+
 #endif
diff --git a/builtin/notes.c b/builtin/notes.c
index 63f95fc554..0423480827 100644
--- a/builtin/notes.c
+++ b/builtin/notes.c
@@ -19,6 +19,7 @@
 #include "string-list.h"
 #include "notes-merge.h"
 #include "notes-utils.h"
+#include "branch.h"
 
 static const char * const git_notes_usage[] = {
 	N_("git notes [--ref <notes-ref>] [list [<object>]]"),
@@ -825,10 +826,15 @@ static int merge(int argc, const char **argv, const char *prefix)
 		update_ref(msg.buf, default_notes_ref(), result_sha1, NULL,
 			   0, UPDATE_REFS_DIE_ON_ERR);
 	else { /* Merge has unresolved conflicts */
+		char *existing;
 		/* Update .git/NOTES_MERGE_PARTIAL with partial merge result */
 		update_ref(msg.buf, "NOTES_MERGE_PARTIAL", result_sha1, NULL,
 			   0, UPDATE_REFS_DIE_ON_ERR);
 		/* Store ref-to-be-updated into .git/NOTES_MERGE_REF */
+		existing = find_shared_symref("NOTES_MERGE_REF", default_notes_ref());
+		if (existing)
+			die(_("A notes merge into %s is already in-progress at %s"),
+			    default_notes_ref(), existing);
 		if (create_symref("NOTES_MERGE_REF", default_notes_ref(), NULL))
 			die("Failed to store link to current notes ref (%s)",
 			    default_notes_ref());
diff --git a/t/t3320-notes-merge-worktrees.sh b/t/t3320-notes-merge-worktrees.sh
new file mode 100755
index 0000000000..1f71d589f5
--- /dev/null
+++ b/t/t3320-notes-merge-worktrees.sh
@@ -0,0 +1,72 @@
+#!/bin/sh
+#
+# Copyright (c) 2015 Twitter, Inc
+#
+
+test_description='Test merging of notes trees in multiple worktrees'
+
+. ./test-lib.sh
+
+test_expect_success 'setup commit' '
+	test_commit tantrum
+'
+
+commit_tantrum=$(git rev-parse tantrum^{commit})
+
+test_expect_success 'setup notes ref (x)' '
+	git config core.notesRef refs/notes/x &&
+	git notes add -m "x notes on tantrum" tantrum
+'
+
+test_expect_success 'setup local branch (y)' '
+	git update-ref refs/notes/y refs/notes/x &&
+	git config core.notesRef refs/notes/y &&
+	git notes remove tantrum
+'
+
+test_expect_success 'setup remote branch (z)' '
+	git update-ref refs/notes/z refs/notes/x &&
+	git config core.notesRef refs/notes/z &&
+	git notes add -f -m "conflicting notes on tantrum" tantrum
+'
+
+test_expect_success 'modify notes ref ourselves (x)' '
+	git config core.notesRef refs/notes/x &&
+	git notes add -f -m "more conflicting notes on tantrum" tantrum
+'
+
+test_expect_success 'create some new worktrees' '
+	git worktree add -b newbranch worktree master &&
+	git worktree add -b newbranch2 worktree2 master
+'
+
+test_expect_success 'merge z into y fails and sets NOTES_MERGE_REF' '
+	git config core.notesRef refs/notes/y &&
+	test_must_fail git notes merge z &&
+	echo "ref: refs/notes/y" >expect &&
+	test_cmp .git/NOTES_MERGE_REF expect
+'
+
+test_expect_success 'merge z into y while mid-merge in another workdir fails' '
+	(
+		cd worktree &&
+		git config core.notesRef refs/notes/y &&
+		test_must_fail git notes merge z 2>err &&
+		grep "A notes merge into refs/notes/y is already in-progress at" err
+	) &&
+	test_path_is_missing .git/worktrees/worktree/NOTES_MERGE_REF
+'
+
+test_expect_success 'merge z into x while mid-merge on y succeeds' '
+	(
+		cd worktree2 &&
+		git config core.notesRef refs/notes/x &&
+		test_must_fail git notes merge z 2>&1 >out &&
+		grep "Automatic notes merge failed" out &&
+		grep -v "A notes merge into refs/notes/x is already in-progress in" out
+	) &&
+	echo "ref: refs/notes/x" >expect &&
+	test_cmp .git/worktrees/worktree2/NOTES_MERGE_REF expect
+'
+
+test_done