Co-considering the ecology (e.g., habitat use) and evolution (e.g., population genetic structure and diversity) of a species can increase understanding of current population status and inform future management practices. Previous analyses indicate mountain lions (Puma concolor) in California are genetically structured and exhibit extreme variation in population genetic diversity. Although human development may have fragmented gene flow, we hypothesized the remaining habitat available would affect the evolution and population genetic diversity of each population. Our results indicate that amount of suitable habitat is strongly and positively associated with population genetic diversity, notably effective population size. Protected suitable habitat, not just the amount of habitat, had a more apparent positive impact on population genetic diversity. Our asymptotic results suggest that contiguous habitat of ~10,000 km2 may be expansive enough to alleviate the measureable negative evolutionary effects of genetic drift and inbreeding, allowing mountain lion populations to maintain suitable effective population sizes. Five of the nine geographic - genetic mountain lion populations in California fell below this habitat threshold and two of those five populations lack connectivity to nearby populations. Enhancing the ecological conditions via protection of more suitable habitat and facilitating positive evolutionary processes via increased connectivity (e.g., road crossing structures) might ensure these small and/or isolated populations persist into the future. Our results demonstrate the amount and status of suitable habitat influence the evolutionary potential of large carnivores. Our results will inform conservation genetics efforts for mountain lions and other top predator populations, aiding in long-term population viability.