Aim. Study of DNA polymorphism of 7 coenopopulations of Siberian stone pine (Pinus sibirica) growing in theKuznetsk Alatau. Methods. Nuclear microsatellite loci developed for P. sibirica were used as genetic markers. Results. 44 allelic variants were identified from 11 nuclear microsatellite loci, which significantly differ in the composition and frequency of occurrence of the studied P. sibirica coenopopulations. The highest level of allelic diversity is found in loci Ps_80612 and Ps_1502048, where 8 and 7 alleles were identified, respectively. The calculation of the main parameters of genetic diversity showed a relatively low level of polymorphism in the studied samples (NA = 3.078; NE = 1.877; HE = 0.445; HO = 0.401). The assessment of the degree of genetic differences between populations using the Nei genetic distance (DN) showed that, despite the low genetic differentiation (DN varies from 0.019 to 0.061), the differences between them can be traced quite clearly. Conclusions. Differences in the level of genetic polymorphism of P. sibirica is defined by the presence of orographic and phytocoenotic barriers between coenopopulations, as well as a high degree of ecological and anthropogenic extremity of individual growth sites. Keywords: Pinus sibirica, Kuznetsk Alatau, microsatellites, genetic diversity, heterozygosity.