Two species of Ratsnake (Elaphe bairdi and Elaphe obsoleta) inhabit different environments in Texas but come into contact with one another on the southwestern edge of the Edwards Plateau. Morphological intergrades have been described by previous studies, yet no genetic evidence of hybridization has ever been reported. We tested for evidence of hybridization and population structure using geographic data, mitochondrial DNA, and microsatellite markers. Cytochrome-b fragments were analyzed for 23 E. bairdi and 33 Elaphe obsoleta lindheimeri from Texas using maximum parsimony and Bayesian-based approaches. All individuals were subjected to Bayesian assignment probability tests based on six microsatellite loci. Overall, sequence divergence was low within E. o. lindheimeri (0.1–0.5%), and higher within E. bairdi (0.1–2.16%). Significant structuring was recovered from mitochondrial haplotypes but not from microsatellite genotypes. Phenotypic intergrades exhibited intermediate or incongruent species assignments based on their nuclear and mitochondrial genomes, suggesting admixture. However, gene flow between E. bairdi and E. o. lindheimeri remains strictly constrained to the zone of sympatry, and these separate lineages remain intact and independently evolving.