Conservation efforts often use habitat models as surrogates for empirical data on the distribution or population size of target species as well as to predict the efficacy of proposed conservation and management actions. Such a model was used to evaluate preserves for the Palm Springs ground squirrel (Spermophilus tereticaudus chlorus) under a proposed Habitat Conservation Plan in the Sonoran Desert of southern California. The habitat model was developed from expert opinion and data from nonprobability-based sample surveys for ground squirrels. We evaluated the model and tested the underlying assumptions about the ground squirrel's habitat affinities, estimated the occupancy rates and detection probabilities of ground squirrels in modeled habitat, quantified the total area of the proposed preserves occupied by ground squirrels, and tested a priori hypotheses about how occupancy differed among vegetation and substrate types. Occupancy rate varied with vegetation and substrate types and, by repeatedly visiting survey points, we found that detection probability was ∼0.22 (SÊ= 0.05). We found ground squirrels were more likely to occupy mesquite (Prosopis glandulosa variety torreyana) on dunes/hummocks (0.99 ± 0.01) than creosote (Larrea tridentata) on dunes/hummocks (0.33 ± 0.09) or other vegetation/substrate types (≤0.08). Our results suggest that this and comparable habitat models should be refined to incorporate detection probabilities and variation in ground squirrel affinity for different vegetation and substrates. In contrast to the existing habitat model, our data suggested that ground squirrel occupancy rate differed by vegetation/substrate types. We suggest that conservation efforts focus on protecting and enhancing the mesquite hummock/dune system that has largely disappeared over the last 50 years due to agricultural and urban development and a lowering of water tables.