Theme reply comments differently from node comments (Drupal 7)
You will have to use the surrounding classes to target the direct comments. Consider a site with the following structure (this is actually based on drupal.org):

...
&lt;div class="content"&gt;
  &lt;div id="node-01" class="node node-forum clearfix"&gt;
    ... Node content ...
  &lt;/div&gt;
  &lt;section class="comments comment-wrapper"&gt;
    &lt;h2 class="title"&gt;Comments&lt;/h2&gt;  
    &lt;a id="comment-7635897"&gt;&lt;/a&gt;

    &lt;div class="comment clearfix"&gt;
      ... Comment content ... 
    &lt;/div&gt;

    &lt;div class="indented"&gt;&lt;a id="comment-7728095"&gt;&lt;/a&gt;
      &lt;div class="comment comment-by-node-author clearfix"&gt;
        ... Comment reply ...
      &lt;/div&gt;
    &lt;/div&gt;
  &lt;/section&gt;
&lt;/div&gt;
...


Node comments can be targeted with the CSS selector .comment-wrapper &gt; .comment. (only target first level childs).

Replies can be targeted with .indented .comment (target all level childs of indented comments).

So have a look at your site's structure and try a similar approach.