The aim of the research was to analyze the allele pool and its changes in the EAB locus of blood groups of cattle of the Kholmogory breed using absorption crosses with bulls of the Holstein breed. The study was carried out by the method of immunological testing according to the agglutination reaction. The choice of locus is not accidental, because it is currently the most informative in terms of the nomenclature of alleles. The predominance of alleles of the Kholmogory breed (A2'O', E3'G'G'') is noted with an increase in the frequency of occurrence (G2Y2E1'Q') and the appearance of new alleles specific of the Holstein breed (O1A'2J'2K'O', B2Q 'G'G”, E'3G'Q', B1O2B', O4Y2A2', O4D'E3'F2'G'O'G”). Over the past 5 years, the index of genetic similarity between herds of Kholmogory cattle in the Komi Republic has twofold. It was revealed that in the population of Komi Republic introduced new alleles of the Holstein breed, but at the same time, part of the alleles of Kholmogory cattle, originally obtained from the breeding reserve, are conserved. Such alleles are transfered between generations of animals and may indicate the preservation of the genome structure of the original mother breed under conditions of intensive selection. As well as alleles are transmitted when using purebred, as well as Holsteinized sires of the Pechora type of breed. The gene pool of the native Kholmogory breed is unique and requires further study. Groups of antigens form a unique genetic structure of herds, which can serve to identify animals by relationship, as well as breed affiliation, as it is similarly made by microsatellite loci and SNP markers (ISAG standard). Testing was carried out as sires in the amount of >30 heads, and their breeding reserve for more than 5 years (>5925 cows of breeding herds). Groups of antigens make it possible to evaluate the change in the genetic structure of the population of the Kholmogory breed and other breeds of cattle in time slices and obtain information about the breeder's actions when focusing on specific genetic traits and their genetic variability, breeding traits and evaluate inbreeding (antigenic similarity), and not only to determine the relationship of animals