diff --git a/src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm b/src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
index 1eef4d6b29..3cf75b96b6 100644
--- a/src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
+++ b/src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
@@ -197,10 +197,8 @@ sub run {
                                                $old->[$i] = delete $refs{$old->[$i]->{name}};
                                            }
                                        }
-                                       foreach my $newRef (values %refSeqs) {
-                                           if( $refs{$newRef->{name}} ) {
-                                               push @{$old}, $newRef;
-                                           }
+                                       foreach my $name (sort keys %refs) {
+                                           push @{$old}, $refs{$name};
                                        }
                                        return $old;
                                    });
diff --git a/tests/data/volvox_formatted_refseqs/seq/refSeqs.json b/tests/data/volvox_formatted_refseqs/seq/refSeqs.json
index f877745c20..cc1b002d6e 100644
--- a/tests/data/volvox_formatted_refseqs/seq/refSeqs.json
+++ b/tests/data/volvox_formatted_refseqs/seq/refSeqs.json
@@ -1,16 +1,16 @@
 [
    {
-      "length" : 6079,
-      "name" : "ctgB",
+      "length" : 50001,
+      "name" : "ctgA",
       "seqChunkSize" : 20000,
-      "end" : 6079,
+      "end" : 50001,
       "start" : 0
    },
    {
-      "length" : 50001,
-      "name" : "ctgA",
+      "length" : 6079,
+      "name" : "ctgB",
       "seqChunkSize" : 20000,
-      "end" : 50001,
+      "end" : 6079,
       "start" : 0
    }
 ]