The article presents the results of determining the allelic variation of genes of monogenic inherited diseases and some marker genes of economically important traits in a dairy herd by means of the allele-specific PCR and the RFLP (Restriction Fragment Length Polymorphism) method. The research was performed on the material of a successful livestock breeding farm in the Krasnodar region, the educational and experimental farm Krasnodarskoye of the Kuban State Agrarian University. 73 heifers of black motley Holstein breed at the age of 11-12 months were analyzed. The choice of animals was determined by the scientific interests of the project team, and took into account the demanding by the farm specialists of the genetic analysis results. The data obtained will be used in the work of the educational and experimental farm for monitoring and improving the genetic structure of the population. Analysis of literary sources, as well as accounting for the economic viability determined by the breed traits, regional characteristics and organization of the production process at the enterprise allowed to identify the most relevant marker genes. The research had shown that none of all analyzed animals was homozygous by any mutant allele (BLAD, CVM, DUMPS, BC, FXID and BS) and fertility haplotype (HCD, HH1, HH2, HH3, HH4, HH5, HHB and HHD). The monitoring of major genes of quantitative traits (QTL – Quantitative Trait Loci), which included searching for and typing of the genes known and/or associated with productivity of cattle in terms of dairy (CSN3, LGB, PRL, GH, LEP, DGAT1) productivity, showed high diversity of the genetic material. The data obtained are the basis for supporting high-productivity animals with good productivity, and for creating a common system of agricultural animals’ identification.