There's a hypothetical paradise where we write all of our documents with markdown and this is well on the way to being a reality with [readmes][1], [websites][2], [wikis][3] and [documentation][4] but in academic writing, LaTeX reigns supreme.
Alone, markdown isn't much of a competitor. It can't do references, it doesn't understand chapters, it can't generate page numbers, you have to manage tables of contents manually, there's no support for captions or automatic numbering of figures and listings. Markdown wasn't designed with these kinds of complex features in mind --- and rightly so.
Maybe I've just been spoiled by the expressive nature of markdown but I don't enjoy writing LaTeX.
There's a project called [Pandoc][9], which allows you to create convert from one document type to another. We can use pandoc to convert markdown into PDFs and HTML.
If you need to convert files from one markup format into another, pandoc is your swiss-army knife.