Context <p>Large carnivores are facing major impacts of anthropogenic activities in the form of habitat loss and fragmentation. Maintaining functional connectivity by accounting for individual species’ requirements is crucial for the long-term survival of remnant populations.</p> Objectives <p>We assessed the connectivity of three sympatric carnivore species, tiger, leopard and dhole and examined the relationship between genetic distance and landscape resistance to determine multispecies genetic connectivity utilizing resistance optimization.</p> Methods <p>We used microsatellite data, landscape and environmental variables to assess the genetic diversity, gene flow and connectivity of the three species in tiger reserves of Maharashtra, India. We optimized the variables using ResistanceGA and used Circuitscape to show the differential connectivity across the landscape.</p> Results <p>The genetic differentiation was highest in dholes and lowest in leopards. Isolation by distance proved to be the significant factor affecting the tiger and leopard connectivity, while for dholes, evapotranspiration was the most significant variable. Our results revealed the strongest impact of habitat fragmentation on dholes followed by tigers and leopards. Anthropogenic factors reduced genetic connectivity for dholes, while geographical distance and environmental variables influenced felid’ connectivity. Connectivity mapping revealed high movement across the landscape for leopards, while for dholes and tigers higher movement was found only around the areas surrounded by smaller forested patches.</p> Conclusions <p>Landscape genetic patterns are a response to ecological differences in habitat characteristics, disturbance, and have a differential impact on genetic structure. This study highlights the need for targeted connectivity models that prioritize the habitat needs of the most vulnerable species.</p>