Understanding how genetic diversity is spatially structured is a priority to gain insights into populations’ genetic status and to assess their abilities to counteract the effects of genetic drift. Such knowledge is particularly scarce for the snow leopard, the wide-ranging felid of Central Asia mountains. Focusing on a snow leopard population from Gansu Province, China, we investigated the presence and strength of spatial genetic patterns in the Qilian mountains, adopting spatially-explicit indices of diversity and multivariate analysis methods. We compared the information contained in two datasets, differing in the number of loci and individuals, through different inertia levels of Principal Component Analysis. Overall, genetic patterns were significantly spatially structured, characterized by a broad geographical division coupled with a fine scale cline of differentiation. Admixed patterns were seen in two adjoining core areas, which were characterized by higher effective population size and higher allelic diversity, compared to peripheral localities. The power to detect significant spatial relationships depended primarily on the number of loci, and secondly on the number of PCA axes used to describe such patterns. Spatial results and indices of diversity highlighted the cryptic structure of snow leopard genetic diversity, driven by its ability to disperse over large distances, thus limiting the isolation effects of both geographic distance and landscape resistance. This study provides insights into the complexity of spatial genetic patterns for a wide-ranging carnivore, providing an extensive baseline on microsatellite polymorphisms which will ultimately guide the implementation of further genetic surveys intended to complement this assessment.