The Evolutionary Biology group at SDSU supports one of the strongest Evolutionary MS programs in the United States, particularly in the realm of Systematics (e.g., see external comments here). If you think that a MS degree is right for you, please consider us further. I have sponsored many stellar MS students while at SDSU – these students have subsequently entered excellent PhD programs (e.g., Univ British Columbia, UC Berkeley, U Arizona, LSU), or have landed good jobs (e.g., 3 of my former students work here).
For students interested in a PhD, the EBPA now supports a joint-PhD program with UC Riverside. This program offers students a unique opportunity to take advantage of excellent faculty members, courses and facilities at two geographically-proximate campuses.