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Global warming is predicted to affect the evolutionary potential of natural populations. We assessed genetic diversity of 25 populations of desert bighorn sheep (Ovis canadensis nelsoni) in southeastern California, where temperatures have increased and precipitation has decreased during the 20th century. Populations in low‐elevation habitats had lower genetic diversity, presumably reflecting more fluctuations in population sizes and founder effects. Higher‐elevation habitats acted as reservoirs of genetic diversity. However, genetic diversity was also affected by population connectivity, which has been disrupted by human development. Restoring population connectivity may be necessary to buffer the effects of climate change on this desert‐adapted ungulate.