Abstract: The snow leopard population in Union Territory of Ladakh (UTL), India is at the centre of five out of eight mountain ranges within the species' habitat in the high-mountain Asia. Its strategic location is of immense conservation significance to maintain genetic connectivity and metapopulation dynamics of snow leopards (Panthera uncia). Therefore, we provide the first estimates of the snow leopard's individual-based spatial genetic characteristics from UTL. Multi-locus genotyping (n = 14 loci) of individuals (n = 19) revealed moderate genetic diversity in the population (mean number of alleles = 5.86 ± 0.55, observed heterozygosity = 0.48 ± 0.05, expected heterozygosity = 0.65 ± 0.03, allelic richness = 2.65 ± 0.15). We did not observe any evidence of population structuring (using STRUCTURE and Factorial Correspondence Analysis) or isolation by distance. However, the clustering approach based on genetic distance (Nei's standard distance and Cavalli-Sforza and Edwards distance) and subsequent discriminant analysis of principal components (DAPC) revealed three sub-clusters of related individuals within the study population without any spatial correlates. We observed 1.2% first-order relatives, suggesting sufficient dispersal and panmixia in the UTL population. We observed high fixation index (FIS = 0.26 ± 0.05; 0.17 ± 0.03 upon removing loci with null alleles) and presence of individuals from genetically divergent populations in UTL. Hence, the high positive FIS value could be attributed to both Wahlund effect and inbreeding. Prioritization and effective conservation planning of the UTL population as a source would benefit the global snow leopard population by (i) maintaining connectivity between the Himalayas and the central Asian mountain ranges, and (ii) providing refuge during future climate change-related range contraction.