Self-incompatibility is one of the most important mechanisms used by flowering plants to prevent self-fertilization and, consequently, to provide the genetic diversity of population. The self-incompatibility in Prunus is controlled by two genes as minimum: S (self-incompatibility) and SFB (S haplotype-specific F-box protein). S gene is represented in the population by a multiple allele series. Compatibility in pollination is dependent on the S allele combination of the cultivars. When S allele in the pollen is identical with one of the S alleles of the mother plant fertilization is arrested. Thus, both self-fertilization and fertilization by pollen of closely related plants (having identical S alleles) are prevented. This mechanism may be interrupted in the case of mutations in the S or SFB gene, which leads to the appearance of self-compatibility cultivars, and polyploidization, such as in sour cherry. The investigation of the S gene allele polymorphism of sweet cherry cultivars of VNIISPK breeding was performed as a part of the study of the gene collection of stone crops. Both consensus (PaConsI, PaConsII) and allele-specific (S1, S5, S9, S10) primers were used. The S-genotype of cultivars Adelina (S3/S5), Poezia (S3/S5), Siana (S3/S6), Orlovskaia feia (S3/S5) and Trosnianskaia (S5/S6) were established. The S-genotype of cultivars Malish, Podarok Orlu, Orlovskaia rozovaia and Orlovskaia yantarnaia was determined partially, as these cultivars have unique previously undescribed or very rare S alleles. Podarok Orlu variety has S9 allele and undescribed one. Malish and Orlovskaia yantarnaia varieties have S6 allele and S17 or S30 alleles supposedly, for these alleles specific primers have not yet been developed. Orlovskaya rozovaia has S6 allele and undescribed previously one.