One of the most important tasks of improvement of horse breeds is investigation into genetic determinants responsible for formation of high productivity and use of genetic monitoring upon selection control. Nowadays genome selection is the most advanced estimation method of breeding abilities. This article presents results of genetic testing of DNA of Mugalzhar horses by 16 microsatellite loci, from 5 to 13 alleles have been identified. Genetic diversity (Nv) of modern population of purebred brood horses was at the level of 7.882, polymorphism (??) equalled to 4.457, heterozygosity (??)-to 0.754, ??-to 0.775, fixation index (Fis)-to 0.027; it referred to a cluster of native/local breeds. Polymorphism varied from 2.785 to 7.442; actually observed heterozygosity from 0.138 to 0.931; theoretically expected one-from 0.641 to 0.866. The number of active alleles in population (Na) was equal to 134.0.