This study uses allele frequency and genotype array data from allozyme electrophoresis to investigate the phylogeographic and taxonomic affinities of groups within the salamander genus Pseudobranchus. Phylogenetic and population genetic analyses of the allozyme data confirm the validity of the two currently recognized species (Pseudobranchus axanthus from peninsular Florida and Pseudobranchus striatus from central and northern Florida, Georgia, and South Carolina). In concert with biogeographic data for other freshwater taxa, these analyses further support the recognition of western, southeastern, and northeastern phylogeographic groups within P. striatus. These species and phylogeographic groups offer new insights into the evolutionary history of this endemic genus in the southeastern United States and the taxonomic status of its nominal subspecies.