The snow leopard is one of the most endangered large mammals. Its population, already low, is declining, most likely due to the consequences of human activity, including a reduction in the size and number of suitable habitats. With climate change, habitat loss may escalate, because of an upward shift in the tree line and concomitant loss of the alpine zone, where the snow leopard lives. Migration between suitable areas, therefore, is important because a decline in abundance in these areas may result in inbreeding, fragmentation of populations, reduction in genetic variation due to habitat fragmentation, loss of connectivity, bottlenecks or genetic drift. Here we use our data collected in Nepal to determine the areas suitable for snow leopards, by using habitat suitability maps, and describe the genetic structure of the snow leopard within and between these areas. We also determine the influence of landscape features on the genetic structure of its populations and reveal corridors connecting suitable areas. We conclude that it is necessary to protect these natural corridors to maintain the possibility of snow leopards' migration between suitable areas, which will enable gene flow between the diminishing populations and thus maintain a viable metapopulation of snow leopards.