Scarlet Snakes (Cemophora coccinea) are monotypic, poorly studied, semifossorial habitat specialists from southeastern United States that traditionally include three subspecies based on color pattern and morphology. We sequenced two mitochondrial and two nuclear loci for 62 individuals from across the species range, and analyzed data with the use of parsimony and Bayesian phylogenetic methods to test a previously proposed phylogenetic hypothesis for C. coccinea. Our results suggest two Pliocene or Pleistocene refugia for Cemophora, one in southern Texas, and the other in the region extending from southeastern Louisiana through Florida. In light of our results we elevate Cemophora coccinea lineri to a full species, C. lineri, that differs from C. coccinea sensu stricto genetically and phenotypically.