The Black-tailed Rattlesnake (Crotalus molossus Baird and Girard, 1853) is a wide-ranging species complex with representatives from the southwestern United States through the highlands of central and southern Mexico. The systematics of this group has received little attention and in the past six decades only two taxonomic changes have been proposed (the transfer of C. basiliscus oaxacus to C. molossus and the elevation of C. m. estebanensis to full species). However, a recent revision of the Neotropical Rattlesnakes (C. durissus and C. simus) recovered a polyphyletic C. molossus. We sequenced data from three mitochondrial genes (ATPases 8 and 6, cyt b, and ND4) and three nuclear genes (c-mos, EXPH5, and RAG1) to examine phylogenetic relationships among C. molossus lineages and the closely related species C. basiliscus and C. totonacus. Results recovered strong support for two deeply divergent northern C. molossus lineages that are morphologically distinct. Biogeographical patterns and divergence dates inferred from mitochondrial data suggest the diversification of C. molossus is the result of a Neogene vicariance event associated with uplift of the Sierra Madre Occidental. Population-level analyses suggest that major lineages of C. molossus have been stable since their initial divergence. On the basis of morphological and molecular evidence we resurrect the name Crotalus ornatus Hallowell, 1854 for Black-tailed Rattlesnake populations in the Chihuahuan Desert and central Texas, USA.