Habitat fragmentation represents the single greatest conservation challenge of the 21st century. This problem is particularly acute for large, obligate carnivores like pumas Puma concolor which have persisted in North and South America in the face of habitat fragmentation and other anthropogenic disturbances. Shrinking habitat and reduced connectivity mean that mapping habitat is increasingly important for species conservation in multiple-use landscapes. Previous work suggests that pumas occupy habitats where sufficient stalking cover and preferred prey are present, yet the intersection of these factors has rarely been assessed. Here we used data from 68 299 camera trap nights collected from 181 sites throughout the San Francisco Bay Area over a four-year period to identify key predictors of habitat occupancy for pumas and their primary prey (mule deer Odocoileus hemionus). Our goal was to determine whether pumas occupy habitats based on relative measures of prey availability (detection frequency), or ease of predation (density of stalking cover) and whether these predictors changed between seasons. Our results indicated that pumas primarily occupied forested habitats and did not choose habitats with abundant deer. Instead, pumas preferentially occupy habitats that facilitate their stalk and ambush hunting strategy, rather than higher prey densities, per se. The best occupancy models for mule deer indicated the importance of roads and shrub cover. However, even the best deer models performed poorly compared to the puma models, likely due to the ubiquity of mule deer in the region. Although prey density is a widely accepted correlate of habitat quality for many carnivores, our results suggest that structural elements of habitat may be a more important variable in predicting habitat use by large stalk and ambush predators like pumas, which has important implications for conservation success