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I'm not sure this is a real answer, but have you tried PHP-markdown-extra (by the very same Michel Fortin)? At least for me (using Mark Jaquith's markdown-on-save plugin) your example is not a problem. But Markdown-extra is not perfect either and I've seen some other quirks with respect to emphasis, e.g. Let $(y_n)_{n\in \omega}$ enumerate ${ x_i: i \in ...