Abstract <p>Using microsatellite markers (SSR), the genetic polymorphism of five coenopopulations of Siberian larch (<i>L. sibirica</i>) growing in the Republic of Khakassia was assessed. The highest values of the average number of alleles per locus were found in coenopopulations of <i>L. sibirica</i> from the steppe meadows of the valley of Lake Fyrkal (3.9 ± 0.458) and forested upland slopes in the valley of Lake Agaskyr (3.9 ± 0.348). The latter coenopopulation is also characterized by the maximum value of the effective number of alleles per locus (2.302 ± 0.283) and the highest rates of observed and expected heterozygosity (<i>H</i>_O = 0.487 ± 0.074, <i>H</i>_E = 0.492 ± 0.070). Analysis of the population structure indicates a 0.8% excess of heterozygous genotypes relative to the population (<i>F</i>_IS = –0.008 ± 0.031) and a 3.4% deficiency of heterozygous genotypes (<i>F</i>_IT = 0.034 ± 0.034) relative to the species. The differentiation of the studied coenopopulations of <i>L. sibirica</i> by SSR markers is 4.3% (<i>F</i>_ST = 0.043). The smallest genetic distance (0.036) was detected between ecotopically most similar (forest) coenopopulations of <i>L. sibirica</i>, and the largest genetic distance (0.077), on the contrary, was identified between ecotopically contrasting (swamp and steppe) coenopopulations.</p>