<p>The snow leopard (<i>Panthera uncia</i>) is the apex predator of cold desert high altitude ecosystems of Asia. Snow leopard populations which inherently occur at low densities are declining across their distribution range due to anthropogenic causes and reduction in prey. Ladakh typifies snow leopard habitat of the trans-Himalayas with high mountain ranges, productive valley habitats, interspersed with human settlements, and sustains a substantial snow leopard population. We used non-invasive sampling of fecal DNA from 72 individual snow leopards and a panel of nine microsatellites to study genetic diversity, population structure, and gene-flow. Scientific understanding of these aspects will provide insights into managing the snow leopard population in light of the rapid development planned for the region We found moderate levels of genetic diversity (H_o = 0.50, H_e = 0.68, MNA = 4.56) with no evidence of population structuring in the Ladakh landscape. Bayesian and non-Bayesian clustering analysis identified low levels of genetic differentiation with high levels of gene flow between the sampling locations indicating the absence of any geographical barriers to the snow leopard dispersal. Migration rates analysis showed high estimates of recent migration between the sampled populations, with Hemis-Leh population located in the centre of Ladakh receiving maximum immigrants. Our results bode well for the species and show that there were no natural barriers to snow leopard movement across the landscape of Ladakh and likely across the trans-Himalayas.</p>