diff --git a/freelinking.module b/freelinking.module
--- a/freelinking.module
+++ b/freelinking.module
@@ -72,6 +72,9 @@
 
         // default freelink (no colon)
         if (strpos($match[1], ':') === FALSE) {
+          if ($syntax == 'markdown' && preg_match('!(\.\.?)?/!', $match[1])) {
+            continue; // it's a regular markdown link
+          }
           $current_plugin = $defaultplugin;
           $target = $match[1];
         } // end default freelink
@@ -86,6 +89,9 @@
                 $current_plugin = $plugin;
             }
           }// end looping through plugins
+          if (!$current_plugin & $syntax == 'markdown') {
+            continue; // it's a regular markdown link
+          }
         } // end non-default freelinks
         $target = freelinking_parse_target($target, $current_plugin);
         $link = freelinking_get_freelink($current_plugin, $target);