This dataset provides the environmental explanatory variables used to explore spatial patterns in species-environment relationships in Gopherus agassizii and Gopherus morafkai across the subregion encompassing the genetic sampling locations used by Edwards et al. (2015). This region offered an opportunity to explore habitat selection across the ecotone between the Mojave and Sonoran deserts and the secondary contact zone between G. agassizii and G. morafkai, and is referred to as the focal study area. The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to identify multivariate clusters and map them back to geographic space. Inman et al. 2019. Local niche differences predict genotype associations in sister taxa of desert tortoise. Diversity and Distributions. xxx.xxx