diff -rupN taxonomy_dhtml_old//taxonomy_dhtml.admin.inc taxonomy_dhtml/taxonomy_dhtml.admin.inc
--- taxonomy_dhtml_old//taxonomy_dhtml.admin.inc	2008-12-13 08:54:10.000000000 +1100
+++ taxonomy_dhtml.admin.inc	2009-03-16 12:02:37.000000000 +1100
@@ -23,6 +23,14 @@ function taxonomy_dhtml_admin() {
     $form[$vocabulary->vid]['noi'] = array('#type' => 'textfield', '#size' => 3, '#maxlength' => 3, '#default_value' => (is_null($vocabulary->noi) ? 25 : $vocabulary->noi));
     $form[$vocabulary->vid]['exposeBlock'] = array('#type' => 'checkbox', '#default_value' => is_null($vocabulary->expblock) ? FALSE : $vocabulary->expblock);
     $form[$vocabulary->vid]['depth'] = array('#type' => 'select', '#default_value' => is_null($vocabulary->depth) ? 0 : $vocabulary->depth, '#options' => array('0' => t('None'), '1' => '1', '2' => '2', '3' => '3', '4' => '4', '5' => '5', '6' => '6', '7' => '7', '8' => '8', '9' => '9', '10' => 'All'));
+    // If the taxonomy_redirect module is available make the option a checkbox.  Otherwise make it hidden.
+    // This makes sure that if the form is saved when taxonomy_redirect is not enabled the value in the taxonomy_redirect field isn't lost 
+    if (module_exists('taxonomy_redirect')) {
+      $form[$vocabulary->vid]['taxonomy_redirect'] = array('#type' => 'checkbox', '#default_value' => is_null($vocabulary->taxonomy_redirect) ? FALSE : $vocabulary->taxonomy_redirect);
+    }
+    else {
+      $form[$vocabulary->vid]['taxonomy_redirect'] = array('#type' => 'hidden', '#value' => is_null($vocabulary->taxonomy_redirect) ? FALSE : $vocabulary->taxonomy_redirect);
+    }
   }
 
   $form['submit'] = array('#type' => 'submit', '#value' => t('Save'));
@@ -46,6 +54,7 @@ function theme_taxonomy_dhtml_admin($for
       $row[] = drupal_render($vocabulary['noi']);
       $row[] = drupal_render($vocabulary['depth']);
       $row[] = drupal_render($vocabulary['exposeBlock']);
+      $row[] = drupal_render($vocabulary['taxonomy_redirect']);
       $rows[] = array('data' => $row, 'class' => 'draggable');
     }
   }
@@ -53,7 +62,12 @@ function theme_taxonomy_dhtml_admin($for
     $rows[] = array(array('data' => t('No vocabularies available.'), 'colspan' => '3'));
   }
 
-  $header = array(t('Name'), t('Number of items to display'), t('Depth'), t('Expose Block'));
+  if (module_exists('taxonomy_redirect')) {
+    $header = array(t('Name'), t('Number of items to display'), t('Depth'), t('Expose Block'), t('Use taxonomy redirect'));
+  }
+  else {
+    $header = array(t('Name'), t('Number of items to display'), t('Depth'), t('Expose Block'));
+  }
   return theme('table', $header, $rows, array('id' => 'taxonomy')) . drupal_render($form);
 }
 
@@ -67,7 +81,7 @@ function taxonomy_dhtml_admin_submit($fo
   foreach (array_keys($form_state['values']) as $ak) {
     if (is_array($form_state['values'][$ak])) {
       db_query("DELETE FROM {taxonomy_dhtml} WHERE vid=%d", $ak);
-      db_query("INSERT INTO {taxonomy_dhtml} (vid, noi, depth, expblock) VALUES (%d, %d, %d, %d)", $ak, $form_state['values'][$ak]['noi'], $form_state['values'][$ak]['depth'], $form_state['values'][$ak]['exposeBlock']);
+      db_query("INSERT INTO {taxonomy_dhtml} (vid, noi, depth, expblock, taxonomy_redirect) VALUES (%d, %d, %d, %d, %d)", $ak, $form_state['values'][$ak]['noi'], $form_state['values'][$ak]['depth'], $form_state['values'][$ak]['exposeBlock'], $form_state['values'][$ak]['taxonomy_redirect']);
     }
   }
   cache_clear_all();
diff -rupN taxonomy_dhtml_old//taxonomy_dhtml.install taxonomy_dhtml/taxonomy_dhtml.install
--- taxonomy_dhtml_old//taxonomy_dhtml.install	2008-12-13 08:54:10.000000000 +1100
+++ taxonomy_dhtml.install	2009-03-16 11:09:00.000000000 +1100
@@ -28,6 +28,12 @@ function taxonomy_dhtml_update_6100() {
   return $ret;
 }
 
+function taxonomy_dhtml_update_6101() {
+  $ret = array();
+  db_add_field($ret, 'taxonomy_dhtml', 'taxonomy_redirect', array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'description' => t('Whether or not to use taxonomy redirect for the menu links.'), 'default' => 0));
+  return $ret;
+}
+
 /**
  * Implementation of hook_schema().
  */
@@ -63,6 +69,13 @@ function taxonomy_dhtml_schema() {
         'description' => t('Boolean to indicate if we are making this available on the block page.'),
         'default' => 0,
       ),
+      'taxonomy_redirect' => array(
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'description' => t('Whether or not to use taxonomy redirect for the menu links.'),
+        'default' => 0,
+      ),
     ),
   );
 
diff -rupN taxonomy_dhtml_old//taxonomy_dhtml.module taxonomy_dhtml/taxonomy_dhtml.module
--- taxonomy_dhtml_old//taxonomy_dhtml.module	2008-12-13 08:54:10.000000000 +1100
+++ taxonomy_dhtml.module	2009-03-16 12:03:19.000000000 +1100
@@ -58,15 +58,21 @@ function taxonomy_dhtml_vocab_vert($voca
  * The depth at which we are processing.  We stop recursion if this is zero.
  */
 function taxonomy_dhtml_process_term($term, $depth) {
+  $dhtml_vocab = taxonomy_dhtml_get_vocabulary($term->vid);
+  $use_taxonomy_redirect = FALSE;
+  if (module_exists('taxonomy_redirect') && $dhtml_vocab) {
+    $use_taxonomy_redirect = TRUE;
+  }
+
   switch ($depth) {
     case 0:
-      $url = "taxonomy/term/$term->tid";
+      $url = $use_taxonomy_redirect ? taxonomy_term_path($term) : "taxonomy/term/$term->tid";
       break;
     case 10:
-      $url = "taxonomy/term/$term->tid/all";
+      $url = $use_taxonomy_redirect ? taxonomy_term_path($term) : "taxonomy/term/$term->tid/all";
       break;
     default:
-      $url = "taxonomy/term/$term->tid/$depth";
+      $url = $use_taxonomy_redirect ? taxonomy_term_path($term) : "taxonomy/term/$term->tid/$depth";
   }
 
   $count = taxonomy_dhtml_term_count_nodes($term, $depth);
@@ -113,6 +119,7 @@ function taxonomy_dhtml_help($path, $arg
     case 'admin/settings/taxonomy_dhtml':
       $output = '<p>';
       $output .= "This module provides a DHTML representation of this site's taxonomy. ". l("Blocks", "admin/build/block"). " are also provided for each vocabulary.";
+      $output .= (module_exists('taxonomy_redirect')) ? " Check the 'Use taxonomy redirect' checkbox if you would like ". l("Taxonomy Redirect", "admin/build/taxonomy_redirect"). " to override the links in your menu." : "";
       return $output;
   }
 }
@@ -141,10 +148,10 @@ function taxonomy_dhtml_get_noi($vid) {
  */
 function taxonomy_dhtml_get_vocabularies($exposed = FALSE) {
   if ($exposed) {
-    $result = db_query(db_rewrite_sql('SELECT v.*, t.noi, t.depth, t.expblock FROM {vocabulary} v LEFT JOIN {taxonomy_dhtml} t ON v.vid = t.vid WHERE t.expblock=1 AND t.noi>0 ORDER BY v.weight, v.name', 'v', 'vid'));
+    $result = db_query(db_rewrite_sql('SELECT v.*, t.noi, t.depth, t.expblock, t.taxonomy_redirect FROM {vocabulary} v LEFT JOIN {taxonomy_dhtml} t ON v.vid = t.vid WHERE t.expblock = 1 AND t.noi > 0 ORDER BY v.weight, v.name', 'v', 'vid'));
   }
   else {
-    $result = db_query(db_rewrite_sql('SELECT v.*, t.noi, t.depth, t.expblock FROM {vocabulary} v LEFT JOIN {taxonomy_dhtml} t ON v.vid = t.vid ORDER BY v.weight, v.name', 'v', 'vid'));
+    $result = db_query(db_rewrite_sql('SELECT v.*, t.noi, t.depth, t.expblock, t.taxonomy_redirect FROM {vocabulary} v LEFT JOIN {taxonomy_dhtml} t ON v.vid = t.vid ORDER BY v.weight, v.name', 'v', 'vid'));
   }
 
   $vocabularies = array();
@@ -157,6 +164,23 @@ function taxonomy_dhtml_get_vocabularies
 }
 
 /**
+ * Retrieve a taxonomy_dhtml vocabulary object.
+ *
+ * @param vid
+ *   The vocabulary ID of the taxonomy_dhtml vacabulary object you want to retrieve.
+ *
+ * @return
+ *   A taxonomy_dhtml vocabulary object or FALSE if there wasn't one that matched the given vid.
+ */
+function taxonomy_dhtml_get_vocabulary($vid) {
+  $result = db_query("SELECT * FROM {taxonomy_dhtml} v WHERE v.vid = '%s'", $vid);
+
+  $vocab = db_fetch_object($result);
+
+  return $vocab;
+}
+
+/**
  * Retrieve term count recursively
  * Rewrite of taxonomy_term_count_nodes to allow us to eliminate children from the count.
  *