diff --git a/src/JBrowse/Browser.js b/src/JBrowse/Browser.js
index b4528a7bf8..ee07fe163f 100644
--- a/src/JBrowse/Browser.js
+++ b/src/JBrowse/Browser.js
@@ -743,7 +743,7 @@ regularizeReferenceName: function( refname ) {
                      .replace(/^([a-z]*)0+/,'$1')
                      .replace(/^(\d+|x|y)$/, 'chr$1' )
                      .replace(/^(x?)(ix|iv|v?i{0,3})$/, 'chr$1$2' )
-                     .replace(/^mt$/, 'chrm');
+                     .replace(/^mt?$/, 'chrm');
 
     return refname;
 },
diff --git a/tests/js_tests/spec/RegularizeRefSeqs.spec.js b/tests/js_tests/spec/RegularizeRefSeqs.spec.js
index 31706a1315..e8c32b6b39 100644
--- a/tests/js_tests/spec/RegularizeRefSeqs.spec.js
+++ b/tests/js_tests/spec/RegularizeRefSeqs.spec.js
@@ -58,7 +58,8 @@ describe( 'centralized ref seq name regularization', function() {
         [ 'XIV', 'chrxiv' ] ,
         [ 'XV', 'chrxv' ] ,
         [ 'XVI', 'chrxvi' ] ,
-        [ 'mt', 'chrm' ]
+        [ 'mt', 'chrm' ],
+        [ 'M', 'chrm' ]
     ];