Large herbivores play an important role in species-based and site-based conservation approaches in the country. The success of these approaches depends on reducing genetic threats posed by isolation of species in their key habitats. In the present study, we assessed structural connectivity for wild sheep (Ovis gmelini), wild goat (Capra aegagrus), goitered gazelle (Gazella subgutturosa), and Indian gazelle (Gazella bennettii), using species distribution algorithms and connectivity models. Our findings showed that while the distributions of the studied species were correlated to different variables, conservation areas, landscape roughness and grasslands were the most contributing factors in predicting distribution of the species. Majority of habitat patches were located within the boundaries of existing conservation areas, which could be caused by the high environmental resistance outside of conservation areas. Despite the strong structural connectivity in some species, large proportion of migration corridors outside of conservation areas and high degrees of anthropogenic disturbances in natural habitat may reduce functionality of the predicted corridors. The selection of unprotected habitat patches and high-rate migration corridors as Indigenous and Community Conservation Areas (ICCAs) can improve the efficiency of the existing conservation network. The obtained results revealed that the conservation of medium to large-bodied herbivores requires integrated landscape-level management to improve functional connectivity among habitats.