Kramdown is Jekyll's default Markdown interpreter. The Maruku Markdown interpreter is considered obsolete. GitHub Pages Jekyll sites with invalid Markdown or HTML syntax may fail to build if you use the Maruku interpreter.
By default, GitHub Pages Jekyll sites use the kramdown Markdown interpreter. Previously, Jekyll used the Maruku Markdown interpreter, but in October 2012, the Maruku maintainers shut down the project.
Upgrading to kramdown
If you've had a GitHub Pages site for a long time, you'll need to upgrade to the new Markdown interpreter. You can upgrade by adding the following to your site's _config.yml file:
markdown: kramdown
This will tell GitHub Pages to use the kramdown Markdown interpreter instead of Maruku. You may also choose to use another interpreter such as Redcarpet; however, those upgrading from Maruku may find kramdown to be a better fit.
Differences between kramdown and Maruku
Maruku and kramdown use Markdown in similar ways. If you're new to kramdown, or just want to brush up on your Markdown, you can check out the quick reference guide or the full documentation. That said, there are a few gotchas—generally highlighted in yellow within the syntax guide.