I added the following to my .emacs. The hook is to convert tabs to spaces to avoid unpleasant surprises with code blocks. For source to ska-untabify see the EmacsWiki

(autoload 'markdown-mode "markdown-mode")
(add-to-list 'auto-mode-alist '("\\.mdwn" . markdown-mode))

(add-hook 'markdown-mode-hook  
           '(lambda () 
               (make-local-hook 'write-contents-hooks) 
                (add-hook 'write-contents-hooks 'ska-untabify nil t)))

;; DavidBremner