The Mojave and Colorado deserts of southern California have been viewed as vast wilderness since early exploration and, until recently, were considered the most untrammeled among western landscapes in the contiguous lower 48 states (United States Department of Agriculture 1893; Leu et al. 2008). However, the factors that define desert wilderness—small human population, temperature differentials that create unrelenting winds, low rainfall, and cloudless skies—are attractive for renewable energy development. The demand for clean, renewable energy is a national and regional priority and has increased demand for large-scale solar and wind farms in the deserts, particularly in California. The need to balance these national and state energy priorities with existing natural resource and land conservation policies has emerged as a landscape-scale land-use planning initiative known as the Desert Renewable Energy Conservation Plan (DRECP). One of the primary goals for the DRECP was to establish Development Focus Areas (DFAs) where high-quality renewable energy potential of up to 20 gigawatts (GW) could be implemented by the year 2040. DFAs were designed to provide expedited project approvals in locations where environmental impacts could be managed and mitigated, and proximity to transmission corridors provides for the efficient dissemination of energy to users. The DRECP also aims to identify protections for natural resources, recreation, and cultural resources. This plan identifies 37 covered species that receive special consideration in the DRECP. Among the special considerations are climate adaptation requirements, such as the ability to maintain population connectivity through wildlife corridors, while protecting several special recreation areas and 32,000 known cultural sites that are dispersed throughout the region. We evaluated several particular aspects of the DRECP design and process. In particular, we examined land designations in relation to published studies on Mohave ground squirrel (Xerospermophilus mohavensis) habitat and genetic diversity patterns of a suite of broadly distributed desert animal species. The squirrel and its habitat are of particular interest because the entire range of the squirrel is encompassed by the DRECP. We describe the framework of the DRECP, provide a case study of how the DRECP accommodates the needs of the Mohave ground squirrel and its habitat, illustrate DFAs in relation to the genetic diversity of a broad range of terrestrial biota, and conclude with some observations on how land-use issues were resolved across the landscape under various scenarios.