Agassiz's Desert Tortoises (Gopherus agassizii) spend >95% of their lives underground in cover sites that serve as thermal buffers from temperatures, which can fluctuate >40°C on a daily and seasonal basis. We monitored temperatures at 30 active tortoise cover sites within the Soda Mountains, San Bernardino County, California, from February 2004 to September 2006. Cover sites varied in type and structural characteristics, including opening height and width, soil cover depth over the opening, aspect, tunnel length, and surficial geology. We focused our analyses on periods of extreme temperature: in summer, between July 1 and September 1, and winter, between November 1 and February 15. With the use of multivariate regression tree analyses, we found cover-site temperatures were influenced largely by tunnel length and subsequently opening width and soil cover. Linear regression models further showed that increasing tunnel length increased temperature stability and dampened seasonal temperature extremes. Climate change models predict increased warming for southwestern North America. Cover sites that buffer temperature extremes and fluctuations will become increasingly important for survival of tortoises. In planning future translocation projects and conservation efforts, decision makers should consider habitats with terrain and underlying substrate that sustain cover sites with long tunnels and expanded openings for tortoises living under temperature extremes similar to those described here or as projected in the future.