These data include environmental covariates used to develop species distribution models for Gopherus agassizii and Gopherus morafkai, along with PCA-reduced environmental covariates used to explore local species-environment relationships within a subregion of the ectone between the two species. We also provide the genotype association used to test the mapped clusters of multiscale geographically weighted regression coefficients against models of (i) a geographically-based taxonomic designation these two sister species, and (ii) an environmental ecoregion designation. These data support the following publication: Inman et al. 2019. Local niche differences predict genotype associations in sister taxa of desert tortoise. Diversity and Distributions. https://doi.org/10.1111/ddi.12927