Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. We gathered new and existing mitochondrial sequences and genome-wide nuclear data for 30 North American squamate species sampled in the North American Coastal Plain and Desert Southwest. We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both mitochondrial and nuclear diversity, while other predictors differed for each dataset.