Skunks usually are identified by their common name (skunk) when submitted for rabies testing. In the desert southwest (Arizona, New Mexico, Texas, USA; and northern Mexico), there are five species of skunks; four of which can occur in sympatry. To better understand the ecology of skunk rabies in these areas, it is imperative that species be properly identified. We used the displacement loop (d-loop) of the mitochondrial genome to identify to species 24 skunk brain samples submitted for rabies testing in New Mexico from 2001 to 2002. Most were identified as striped skunks (Mephitis mephitis), but hooded (Mephitis macroura) and hog-nosed (Conepatus leuconotus) skunks were also found.