The Baird's pocket gopher (Geomys breviceps) is a solitary, fossorial rodent found throughout areas of Texas, Arkansas, Oklahoma, and Louisiana. These rodents are highly modified morphologically for an underground lifestyle, often resulting in limited vagility and isolated populations. Despite these unique characteristics, little is known about the population genetics of pocket gophers. We used mitochondrial and microsatellite data and performed a series of population genetic analyses to better understand the population structure and gene flow among a series of G. breviceps localities. Population genetic analyses supported high levels of gene flow among localities within 2 km of each other, with decreasing levels as distance between localities increased. Findings suggest that 2–3 localities function as one genetic cluster, resulting in a total of 3–4 total genetic clusters observed in this study. Results also suggest that the Baird's pocket gopher is capable of moving at least 2 km, but further analyses should be completed to better understand dispersal distance in this fossorial species.