Loss of wetlands throughout the southeastern United States threatens the persistence of the region's highly diverse freshwater fauna. Losses are especially concerning for rare species that maintain small or fragmented ranges, zoogeographies that characterize many of the region's numerous freshwater endemics. We assayed nuclear and mitochondrial DNA sequence data from the Pine Barrens Treefrog (Hyla andersonii), a rare species distributed across the Atlantic and Gulf coastal plains. We hypothesized that the species' evolutionary history has been associated with changes in wetlands during Quaternary interglacials and that the contemporaneous extent of wetlands is positively correlated with population genetic diversity. Genetic variation was highest in North Carolina and South Carolina and lowest in New Jersey and Florida. Mean times to common ancestry ranged from 132,486 to 1,290,605 yr before present, and effective sizes ranged from 4,241 individuals in New Jersey to 403,718 individuals in North Carolina. Population migration rates were generally very low (<0.01), although higher rates were found between North Carolina and South Carolina. Total area of wetlands varied from 2,482 km² in South Carolina to 7,384 km² in North Carolina and has declined between 2001 and 2016. Genetic diversity was positively, although nonsignificantly, correlated to total amount of wetland habitat. Pine Barrens Treefrog is comprised of four relictual populations associated with ecological changes driven by climatic progressions of Quaternary interglacials, and collectively these populations conform to an abundant center model of evolution. All populations are conservatively designated management units, although evolutionarily significant unit status cannot be discounted.