Background. The S-locus, which controls the system of gametophytic incompatibility in the species of the Rosaceae family, is characterized by a high degree of allelic diversity, which is successfully used for S-genotyping and molecular certification, as well as for clarifying the phylogenetic relationships between species. In practical aspect, the study of the S locus is also important for identifying self-fertility mutations affecting pollen specificity. Recently, an association of this trait with the presence of the S17 allele in the genome of the domestic plum Prunus domestica L. has been established, and specific primers for its identification developed. The aim of our work was to identify markers of this allele in accessions of stone fruit collections maintained at the Maykop Experimental Station – a branch of VIR and the Pushkin and Pavlovsk Laboratories of VIR, and to determine their effectiveness in parallel phenotypic analysis. Materials and methods. Molecular screening was performed using S17 allele specific primers and consensus primers PruC2/PCER. In parallel, over the course of two years (2023 and 2024), plum and cherry plum accessions were phenotyped for self-fertility using the methodology adopted at VIR. Results and discussion. A subset of 266 stone fruit accessions was studied, including 76 accessions of cherry plum Prunus cerasifera Ehrh., 150 accessions of domestic plum P. domestica, one accession of North American plum Prunus americana Marsh., one accession of Canadian plum Prunus nigra Aiton, three samples of Russian plum Prunus× rossica Erem. and 35 of blackthorn Prunus spinosa L. Sixteen accessions were identified as carriers of the S17 allele. In parallel, a significant part of the experimental subset, 124 accessions of domestic plum and cherry plum, was phenotyped, and the ability of plants to form fruits when pollinated with their own pollen assessed. The portion of self-fertile accessions of hexaploid European plum was 56.1%, while for cherry plum only 7.4%. These results are fully consistent with the phenomenon of widespread self-fertile forms among polyploid organisms described in the literature. Most self-fertile accessions did not have the S17 allele, that is, their self-fertility should be explained by some other reasons. On the other hand, almost all accessions of European plum with the S17 allele were self-fertile. Conclusions. Comparison of the molecular screening results and phenotypic analysis data showed that the S17 allele in the domestic plum does indeed exhibit an association with the self-compatibility property, but P. domestica may also have other mutant variants that disrupt the degradation mechanisms of its own pollen tubes. No such association is observed in diploid cherry plum. The self-fertile accessions with markers of the S17 allele identified during the analysis are of great interest for breeding, since they can be directly used in marker-assisted selection.