Таврійський науковий вісник № 108 work is to clarify the question: what exactly factors determine the differences in the chemical composition of the milk of Holstein cows of different ecogenotypes. It is important to establish how much it is possible to use the polymorphism of the above genes in the analysis of the animal gene pool, and to predict the qualitative indicators of milk that meets the requirements of the processing industry. Therefore, the article presents the results of studies of the polymorphism of individual QTL genes and the main signs of milk productivity of Holstein cattle of German, Hungarian and Danish origin in Southern Ukraine. The features of the frequency distribution of these loci and the manifestation of signs of milk production of cows are determined under the conditions of modeling the effects of stabilizing selection according to the classical model and forming five equal in number groups. The conducted studies did not establish an unambiguous dependence of economically valuable traits on the genotypes of individuals at the examined loci. However, according to the CNS3 gene, BB genotypes had higher fat, protein milk yield and milk yield, and heterozygotes for LEP were characterized by large yields. Evaluation of the polymorphism of two structural genes-CSN3 and GH in Holstein cows of different ecogenotypes made it possible to assert that the quality of milk obtained from cows of German and Hungarian origin is better, as evidenced by the relatively high frequencies of the CSN3 B allele. Cows of German origin are a unique ecogenotype for combining a relatively high level of milk yield with significant frequencies of the somatotropin allele L, which resulted in an increased amount of milk fat and protein. Holstein cattle of Danish origin is the most consolidated compared with other ecogenotypes, as evidenced by the values of their actual and expected heterozygosity. This statement is also explained by the calculation of the coefficient of inbreeding. A significant genetic heterogeneity of livestock in the milk direction of the productivity of the modal group has been established, which indicates the possibility of obtaining milk of various chemical composition from them.