Conservation of isolated wetlands is critical for maintaining regional biodiversity within the southeastern U.S. However, relatively little is known about the ecological communities of these wetland systems, particularly within the karst wetlands of the southeastern Coastal Plain. In southwestern Georgia seasonal isolated wetlands include marshes, cypress savannas and cypress/gum swamps, which have fundamental differences in vegetation and soils, hydrology, water chemistry and invertebrate abundance and diversity. We examined the relationship between wetland type and the distribution of amphibians in 28 relatively undisturbed, seasonally flooded isolated wetlands in southwestern Georgia, USA. We sampled wetlands for amphibians in the winter, spring and summer using aquatic traps, dipnetting, PVC pipe refugia and automated frog call recording devices (frogloggers). Mean amphibian species richness among study wetlands was 12.7 ± 0.5 species (range 7–18). Both species richness and composition varied among wetland types, with different wetland types supporting different amphibian assemblages. Our results highlight the importance of wetland diversity in promoting regional amphibian diversity.