I was going to search for that, but here it is posted.
Calibre is going to throw in all sorts of it's preferred .css and markup. In linux pandoc should work, I am playing with it at present. However pandoc will not (as far as I can detemine) go from markdown directly to .epub You will have to go to an intermediate stage, say .html.
Another option is epubmaker. There is more than one epubmaker. The open source python one found at Distributed Proofreaders epubmaker will convert text to .epub (html, .rtf and .pdf also) Note: IT REALLY PREFERS RST as the initial source
https://pypi.python.org/pypi/epubmaker/0.3.19
http://www.pgdp.net/wiki/RST:_EpubMaker_Guide
online version at DP where you can upload raw and see what will result is. Try giving it some markdown.
http://epubmaker.pglaf.org/
epubmakers splits can be a little random.
googling epubmaker marcello removes the commercial epubmaker
Another program that is used by users of Distributed Proofreaders and DPCanada is in perl - guiguts. But it will not convert directly to .epub, again the intermediate .html is the result. The formatting of the raw text that goes to guiguts is close to markdown.
Tcl/Tk gui. If debian - do not follow the dated guides for installation, especially if you follow testing.
For quick and dirty - Calibre is the way to go. For the best "hands on" control for best finished output in open source Sigil is it. But you will need .html to start