Identification of highly biodiverse areas has become a crucial step in protecting species richness, especially considering the rapid collapse of biodiversity and the limited funds available to avert, far less to reverse, these trends. Therefore, we aimed to identify the most important areas for the conservation of specified mammalian groups in Southern Asia, a region rich in biodiversity hotspots threatened by increasing rates of habitat loss and other anthropogenic activities. To achieve this, we modelled the occupancy of ungulates and of small, medium and large carnivorans at 20 study sites across the region and identified hotspots of species richness. We analysed the variation of estimated space use between different species groups and ranked areas according to their predicted importance for mammalian species conservation. Our results reveal a significant positive correlation in the spatial utilization patterns of competitive carnivores, yet no correlation among carnivores and their prey species, suggesting that anthropogenic impacts in the region are constraining species to coexist in only the few remaining suitable areas, superseding interactions between species guilds. Although the rank of site importance varied amongst species groups, we were able to identify a consensus on sites that are crucial for the conservation of all groups considered. Most of these top-ranking sites were located in the peninsular region of Thailand. We argue that, of the areas assessed, these sites represent the most important refuges for species conservation in the region, and their protection is critical for the maintenance of the biodiversity in Southern Asia.