Amphibians are a globally distributed and diverse lineage, but much of our current understanding of their population genetic structure comes from studies in mesic temperate habitats. We characterize the population genetic structure of two sympatric explosive breeding amphibians in the southwestern deserts of the United States: the Great Plains toad (Anaxyrus cognatus) and Couch’s spadefoot toad (Scaphiopus couchii). For both species, we find limited genetic differentiation even between populations in adjacent valleys separated by dispersal barriers such as mountainous habitats. To understand how population genetic patterns in these two arid-adapted species compare to taxa in more mesic environments, we computed a standardized measure of population differentiation for A. cognatus, S. couchii, and for pond-breeding amphibians that inhabit mesic temperate environments. Our results indicate that the arid-adapted species have lower population genetic structure at fine and moderate scales than most other amphibian species we surveyed. We hypothesize that stochasticity in the availability of appropriate breeding sites as well as landscape homogeneity may result in increased population connectivity in desert-adapted frogs. Future work examining fine-scale population structure in amphibians from a diversity of habitats will test the generality of our findings. Intraspecific comparisons among localities with varied seasonality and habitats will be particularly useful for investigating the interaction between species-typical population dynamics and environmental characteristics as determinants of population connectivity in pond-breeding amphibians.