<p>Comprehending the genetic structure of wildlife populations is fundamental for the formulation of effective conservation measures, especially in fragmented and fragile environments like the Himalayas. This study investigates the population genetics of Asiatic black bear (<i>Ursus thibetanus</i>) and Leopard (<i>Panthera pardus</i>) in Himachal Pradesh, an Indian State experiencing escalated anthropogenic influences and large-scale development. Using microsatellite markers and a combination of Bayesian clustering, discriminant analysis of principal components (DAPC), and spatial genetic analyses, we evaluated the patterns of genetic diversity, population structure, gene flow and evidence of isolation by distance (IBD) for these species. The results showed relatively low levels of genetic diversity, with an observed heterozygosity (Ho) of 0.35 and 0.41 for Asiatic black bears and Leopards, respectively. There was no clear evidence of historical genetic bottlenecks, and both species exhibited stable contemporary effective population sizes (204.5 for Asiatic black bear, 208.1 for Leopard), necessary to sustain short-term evolutionary potential. Furthermore, we found low genetic differentiation, high admixture, and asymmetric gene flow across the study region for both the species, with no significant isolation by distance (IBD). Our findings highlight the resilience of these species and emphasize habitat connectivity as a critical factor for sustaining gene flow and long-term population persistence. Our results also underscore the importance of maintaining permeable semi-natural landscapes and mitigating human-wildlife conflict to support the long-term survival of carnivore populations in the Himalayas. This study provides a foundation for future research integrating genetic and ecological approaches to improve understanding of wildlife conservation in the Himalayan ecosystem.</p>