Understanding phylogeographic structure is a key step in examining the processes related to lineage divergence and speciation. It is often expected that wide-ranging taxa will be composed of deeply divergent lineages and that codistributed species will have similar population genetic structure. Within the southeastern coastal plain of North America, a biodiversity hotspot, the evolutionary processes that have led to the accumulation of diversity are underexplored. Several process within this region could be responsible for species diversification, including past changes in climate, fluctuating sea levels, and the formation of river systems. However, it is also possible that a pattern of isolation-by-distance can explain population genetic structure found in widely distributed species, which can serve as a null hypothesis for observed genetic structure. We generate a reduced representation genomic dataset with population level sampling for two sister species of snakes endemic to the southeastern coastal plain, the mudsnakes and rainbow snakes (Farancia abacura and F. erytrogramma, respectively). With these data we find a strong signal of population divergence in F. abacura, while isolation-by-distance alone explains genetic divergence in F. erytrogramma. We also identify several genomic regions associated with environmental variation that may be key to local adaptation. Lastly, we find that the best fit demographic model includes gene flow during the initial divergence of these two species. This model also suggests that there is current unidirectional gene flow from the eastern F. abacura lineage into F. erytrogramma. However, the two F. abacura lineages appear to be reproductively isolated. We suggest further comparative phylogeographic work to understand the full suite of evolutionary processes driving diversification and endemism in the southeastern coastal plain.