Aim Ecological limits on population sizes and the number of species a region can sustain are thought to simultaneously produce spatial patterns in population genetic diversity and species richness due to the effects of random drift operating in parallel across population and community levels. Here, we test the extent to which resource-based environmental limits jointly determine these patterns of biodiversity in amphibians. Location North America. Taxon Amphibians. Methods We repurposed open, raw microsatellite data from 19 species sampled at 554 sites in North America and mapped nuclear genetic diversity at the continental scale. We then tested whether ecological limits defined by resource availability and environmental heterogeneity could simultaneously shape biogeographic patterns in genetic diversity and species richness with structural equation modelling. Results Spatial patterns of population genetic diversity run opposite patterns of species richness and genetic differentiation. However, while measures of resource availability and niche heterogeneity predict 89% of the variation in species richness, these landscape metrics were poor predictors of genetic diversity. Main conclusions Although heterogeneity appears to be an important driver of genetic and species biodiversity patterns in amphibians, variation in genetic diversity both within and across species makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity. This result differs from those found in endotherms and may be due to the considerable life history variation found across amphibians.