Drupal Bootstrap THEME_menu_tree on new menu I'm using Drupal 7 and the Bootstrap theme, in template.php I am successfully theming the primary menu (main menu) to enable extra list styles with

function MYTHEME_menu_tree__primary($variables) {
return '&lt;ul class="custom-style"&gt;' . $variables['tree'] . '&lt;/ul&gt;';
}


I would also like to theme a new menu called "Banner" (menu-banner) but can't access it as expected at

function MYTHEME_menu_tree__menu_banner($variables) {
return '&lt;ul class="custom-style"&gt;' . $variables['tree'] . '&lt;/ul&gt;';
}


The new menu is successfully defined in MYTHEME_preprocess_page in template.php

$menu = menu_navigation_links('menu-banner');
$vars['banner_nav'] = theme('links__menu_banner', array('links' =&gt; $menu));


And I'm able to call it as banner_nav in my page templates.

Is there something I'm missing or is there something specific to Bootstrap that I need to do that's different from the documentation at theme_menu_tree?
This isn't related to Bootstrap. In your preprocessor you're using theme_links, which is unrelated to menus. Your "menu" isn't being output as a menu at all. 

If page preprocessing is necessary, you can try:

function THEMENAME_preprocess_page(&amp;$vars) {
  $menu = menu_tree_all_data('menu-banner');
  $vars['banner_nav'] = menu_tree_output($menu);
}


Or you can render the menu block (these are automatically generated if you have the Blocks module enabled):

function THEMENAME_preprocess_page(&amp;$vars) {
  $block = block_load('menu', 'menu-banner');
  $vars['banner_nav'] = _block_get_renderable_array(_block_render_blocks(array($block)));
}


In page.tpl.php:

&lt;?php print render($banner_nav); ?&gt;


Either will work. 

If you don't need to preprocess the menu, you can simply position it via the Blocks admin UI. 

I hope that helps!