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One of the few imperiled ant species in North America is the Comanche Harvester Ant, Pogonomyrmex comanche. Despite its status, little is known about its natural history throughout its range in the western Gulf Coastal Plain of North America. This study presents a regional phylogeographic analysis of P. comanche across sites in its natural range as a first step to learning more about this species. By using COI genotyping, we discovered that the center of genetic diversity is found in central Texas, which is typical for many species that found refugia in the southern North America during Pleistocene glaciations. Although diversity was slightly lower in northern populations, there was no evidence of recent population expansion into northern latitudes. Rather, some deviations from neutrality were consistent with population contraction in the northern regions (Arkansas, Oklahoma). The high diversity and relative rarity of identical sequences among samples were also consistent with dispersal limitation. The exact mechanisms driving its decline are currently unknown, but a combination of dispersal limitation and habitat loss seem likely causes.