This study provides a comprehensive characterization of the whole genomes of the Kazakh breeds of the Jabe and Аdai, types, as well as the Mugalzhar breed. We performed whole genome sequencing on the BGI platform, mapping the obtained data to the EquCab3.0 horse reference genome. The sequencing results revealed a large number of genetic variants in the genomes of the studied horses, indicating a high level of genetic polymorphism. The largest number of variants was found in intronic regions, as well as in untranslated regions. Among the identified variants, single nucleotide polymorphisms were found to be prevalent both before and after filtering, as well as insertions/deletions, which occur much less frequently. Special attention was paid to the SWT1, PPFIA1, SHROOM2, ANOS1, OR4D10, USP25, and ZNF74 genes, which contained more than 100 variants each. It is assumed that these genes can influence metabolism, endurance, reproductive function, sense of smell, immune response and regulation of gene expression in horses. The obtained data represent a valuable resource for future studies on the adaptive potential of Kazakh horse breeds, as well as for the development of conservation strategies and the optimization of breeding programs.