Agassiz's desert tortoise, Gopherus agassizii, faces threats from climate change. With limited mobility to move long distances to more-suitable habitat as climate change advances, whether protecting tortoises in situ or translocating them out of harm's way, a critical conservation task is identifying refugia, lands that will remain suitable under the current climate and the projected, end of the 21st Century warming and drying. While researchers have modeled tortoise habitat suitability, they have done so at coarse scales and did not identify climate refugia that may become apparent only with a fine-scale approach. It is at that scale that managers can implement measures that will foster habitat protection for tortoises throughout their current range. In this case study, we employed fine-scale habitat suitability modeling to identify current habitat and climate refugia within and surrounding the Marine Corps Air Ground Combat Center (MCAGCC) at Twentynine Palms, California. We modeled nearly 284,000 ha of currently suitable tortoise habitat within an 858,800-ha study area. Projected maximum end-of-the-century summer temperatures could reduce the area of tortoise habitat 55% to 127,650 ha; however, almost 115,800 ha would overlap current tortoise habitat and would serve as climate refugia. Applied elsewhere, where tortoise protection must be balanced with other land uses, this approach could increase the efficacy of conservation for this threatened species. Nevertheless, until validated with field studies, habitat suitability models represent hypotheses as to current and future distributions of appropriate tortoise habitat. These hypotheses should foster additional research identifying whether tortoise densities and demographic structure are more secure and whether tortoises can adapt to shifting climates more effectively within than outside modeled refugia.