Abstract <p>The aim of this study was to assess the genetic diversity and population structure of eight indigenous sheep (<i>Ovis aries</i>) breeds from Altai, Tuva, and Mongolia. DNA samples from 327 individuals were used as material. Their genetic diversity was evaluated using 12 microsatellite markers. A total of 187 alleles were identified in the sample. The number of alleles per locus ranged from 7 to 22, confirming a high level of polymorphism. Analysis of Molecular Variance (AMOVA) revealed that the majority of genetic diversity (&gt;90%) is concentrated within breeds, which is typical for local indigenous populations. Analysis of genetic distances (<i>F</i>_ST) and Discriminant Analysis of Principal Components (DAPC) demonstrated significant differentiation between the breeds studied, allowing for the identification of genetic clusters corresponding to their geographic origin. The results highlight substantial within-population genetic diversity and the unique genetic status of each of the breeds studied, underscoring their value as objects for the conservation of genetic resources and for further breeding.</p>