Markdown is a super simple markup language used to add formatting elements to plain text documents.
Muna uses Markdown because it's lightweight, super fast, easy to read (contrary to HTML) and, most importantly, wildly compatible with other applications. So whatever you create in Muna you can export and use everywhere else.
In the words of its creator, John Grubber:
Markdown is not a replacement for HTML, or even close to it. Its syntax is very small, corresponding only to a very small subset of HTML tags. The idea is not to create a syntax that makes it easier to insert HTML tags. In my opinion, HTML tags are already easy to insert. The idea for Markdown is to make it easy to read, write, and edit prose. HTML is a publishing format; Markdown is a writing format. Thus, Markdown’s formatting syntax only addresses issues that can be conveyed in plain text.