The Texas pocket gopher (Geomys personatus) occurs throughout much of southern coastal Texas. Recent genetic studies clarified phylogenetic relationships within the genus Geomys, but the geographic distribution of lineages of G. personatus in southern Texas remains uncertain. We sampled G. personatus in southern Texas and analyzed cranial morphology and DNA sequence data from the mitochondrial cytochrome b gene. Morphology provided weak discriminatory power for the identification of subspecies. Pocket gophers showed high genetic structure in the region, with low levels of haplotype diversity within sites and few shared haplotypes among sites. Phylogenetic analyses revealed Geomys trapped in mainland Nueces County and Flour Bluff clustered with GenBank sequences of G. p. maritimus. Padre Island samples formed a well-defined subcluster, similar to but distinct from G. p. personatus and G. p. megapotamus sequences. Samples from Kleberg County formed a separate clade, consistently outside of G. personatus; Kimura 2 parameter sequence divergence between Kleberg County and G. personatus was >0.12, and Kleberg County samples were more similar to G. texensis (sequence divergence 0.06–0.08). The Kleberg County samples appear to represent a previously undetected cryptic lineage.