The selection of pollinators when planting plantings in crop production and parental pairs during hybridization in breeding is closely related to the problem of self-incompatibility. The results of numerous studies show that self-incompatibility is realized through a variety of biological mechanisms and is aimed primarily at preventing inbreeding within a population. Self-incompatibility in many species is determined by one S-locus with many S-alleles. In this case, the S-haplotype combines male and female specificity determinants (S-determinants), and pollen recognition occurs due to a molecular allele-specific interaction between them. In representatives of the genus Prunus, self-incompatibility is controlled by the interaction of genes belonging to the S locus, the combination of variants of which forms a specific S haplotype. Molecular S-genotyping methods are based on S-RNase gene sequences, which allow the identification of S-alleles and the classification of varieties with respect to incompatibility groups. To date, 31 S-haplotypes have been identified in sour cherries and sweet cherries, and some of the haplotypes are identical to each other. In sour cherry, 12 functional S-haplotypes and 9 nonfunctional ones have been described. 6 S-haplotypes of sour cherry species have also been described. Mutations that occur not only in the S-RNase and SFB genes, but also in regions not associated with the S-locus can lead to disruption of the self-incompatibility mechanism. Studies on the identification of self-incompatibility alleles of representatives of the Cerasus subgenus were in many cases carried out on the species P. avium L. The formation of self-(in)compatibility of tetraploid genotypes of sour cherry is due to the presence of mutations in the S-locus genes, which lead to the appearance of non-functional S-haplotypes. Self-incompatibility of pollen in sour cherry occurs when one fully functional S-allele in the pollen corresponds to one functional S-haplotype in the pistil. Currently, the study of the mechanism of self-incompatibility continues, and genotyping of sour cherry and sweet cherry varieties is carried out at S-loci. DNA analysis data is promising for predicting the level of compatibility of varieties during pollination and fruit set during hybridization.