How do I use disqus comments in github pages blog (Markdown)?

The easiest and cleanest way to do it is to create a partial with the HTML that disqus provides in your _includes/ folder (e.g. _includes/disqus.html) and then just including it in your posts layout file (e.g. _layouts/post.md):

{% include disqus.html %}

You can see an example here: post layout and disqus partial.

Include the disqus comment in your post.html, and set an identifier for the comment count link:

<div id="disqus_thread"></div>
<script type="text/javascript">
    var disqus_shortname = '<your-disqus-name>'; 
    var disqus_identifier = '{{ page.id }}'; 
...
</script>

In your default.html template include the comment count script:

<script type="text/javascript">
    /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */
    var disqus_shortname = '<your-disqus-name>';
...
</script>

Then add the link to the comments using the data-disqus-identifier attribute, so that the comment count will show up after each post in your blog's main page:

<a href="{{post.id}}" data-disqus-identifier="{{post.id}}">Leave a comment</a>

There is an "official" way to accomplish this task. You can find the Disqus indication at this link. In details, the procedure is the following:

1. Add a variable called comments to the YAML Front Matter (i.e. the header of your post file) and set its value to true. A sample front matter might look like:

    layout: default
    comments: true
    # other options
   

2. Create a new template file (i.e. disqus.html) and put the Universal Embed Code there between {% if page.comments %} and {%- endif -%}.

3. Include the disqus.html file into your post template.

Hope it helps :)

To summarise:

1. Use 3rd comment service Disqus, create one its account
2. Associate your site, that is your github site, with disqus
3. Get Disqus shortname in admin/settings/general/
4. Edit your _config.yml of github, make sure it contains following content:

disqus:
    shortname: <your disqus short name>

5. Make sure there is disqus.html under _includes and it looks like:

   {% if page.comments %}
   <div class="comments">
   <div id="disqus_thread"></div>
   <script type="text/javascript">
   var disqus_shortname = '{{ site.disqus.shortname }}';
   (function() {
   var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
   dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js';
   (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq); })();    
   </script>
   <noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
   </div> 
   {% endif %}
   

   6. Include disqus.html in _layouts/post.html

   7. To enable comment, add comments:true on your post yaml front matter. Disable it by setting comments: false or by not including the comments option at all.