Historically believed to harbor unrecognized diversity, the taxonomy of the declining genus Macrochelys (alligator snapping turtles) is debated. The original species, M. temminckii, was recently split into M. temminckii, M. apalachicolae, and M. suwanniensis. However, the status of M. apalachicolae is contested. In this study, we generated thousands of genome-wide loci to quantify population structure and genetic differentiation across the range of Macrochelys spp. Our data indicate that M. apalachicolae is genetically distinct, with little gene flow between M. apalachicolae and other species, thus adding evidence that M. apalachicolae may be a distinct species. We also find genetic variation partitioned among river drainages, with very high intra- and interspecific genetic divergence among river drainages. We suggest that translocations and re-introductions only move turtles in this genus within their natal river drainages to preserve existing patterns of genetic diversity.