California sea lions (Zalophus californianus) occur along much of the Pacific coast of North America, but the number of breeding areas that are occupied is relatively small. Our understanding of the attributes that make these few sites preferable is currently limited. We quantified habitat characteristics—substrate type and coloration, aspect, slope, curvature of shoreline, and availability of shade, water pools, and resting areas—at 26 sites (7 islands) occupied by sea lions and 33 unused sites (8 islands) distributed throughout the Gulf of California, Mexico. Logistic regression models were used to explore how habitat characteristics explained sea lion occupancy patterns. Models discriminated very well between occupied and unused sites, and showed that occupied locations were more often located in sites with larger-size rocks (odds ratio [OR] = 1.209), lighter-color substrates (OR = 0.219), and convex shorelines (OR = 1.067). All of these preferred characteristics are likely to play a role in the prevention of heat stress in sea lions, suggesting that increases in temperature, such as those expected from global warming, may pose an additional risk for this already declining sea lion population. To partially offset this risk, our results may be used to identify, and protect, unused but suitable (i.e., thermally favorable) habitat. In addition, we recommend effective protection and monitoring of the currently occupied areas and their populations.