The only markdown implementation I know of, that uses an actual parser, is Jon MacFarleane’s peg-markdown. Its parser is based on a Parsing Expression Grammar parser generator called peg.
EDIT: Mauricio Fernandez recently released his Simple Markup Markdown parser, which he wrote as part of his OcsiBlog Weblog Engine. Because the parser is written in OCaml, it is extremely simple and short (268 SLOC for the parser, 43 SLOC for the HTML emitter), yet blazingly fast (20% faster than discount (written in hand-optimized C) and sixhundred times faster than BlueCloth (Ruby)), despite the fact that it isn’t even optimized for performance yet. Because it is only intended for internal use by Mauricio himself for his weblog, there are a few deviations from the official Markdown specification, but Mauricio has created a branch which reverts most of those changes.