Cougars throughout California are under threat due to habitat change, landscape fragmentation, and urban and exurban development. Understanding cougar population sizes and habitat associations within areas of their distribution that are least affected by people (e.g., National Parks, designated wilderness areas) provides a benchmark from which to compare other landscapes and future conditions, informs conservation and management actions, and contributes to cougar persistence. Yosemite National Park in the Sierra Nevada Mountains of California may act as an important refuge for cougars. Despite this, there is no previous estimate of the number of cougars living in Yosemite or an evaluation of habitat selection patterns within the Park. We collected data on cougar distribution in Yosemite detection dog team surveys and infrared trail cameras. We then used spatial capture-recapture modeling to estimate the population size of cougars living in Yosemite and determine habitat associations of cougars in this protected area. Determining cougar population size and habitat associations here may provide critical information for their conservation and management elsewhere in California. Our research represents a critical step in cougar conservation and has important implications for natural resource management.