Display JavaDocs on GitHub

I don't think it's possible to make a usable Javadoc with MarkDown. The best solution is probably to commit the Javadoc you generated on the gh-pages branch (or in the docs/ directory depending on the settings of your project). It will be available at :

http://username.github.io/projectname

Here is an example from one of my projects:

http://ebourg.github.io/jsign/apidocs/

Currently you can also host your Javadoc with Github Pages from not only a gh-pages branch, but directly from the /docs folder within your master branch. You can check the help section on this topic, here (also check attached image below).

Also, there's a project on Github that targets some conversion of Javadoc to Markdown (have not tried it yet, just leaving the reference).