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The pollination of self-incompatible diploid sweet cherry is determined by the S-locus alleles. We resolved the S-alleles of 50 sweet cherry cultivars grown in Estonia and determined their incompatibility groups, which were previously unknown for most of the tested cultivars. We used consensus primers SI-19/20, SI-31/32, PaConsI, and PaConsII followed by allele-specific primers and sequencing to identify sweet cherry S-genotypes. Surprisingly, 48% (24/50) of the tested cultivars, including 17 Estonian cultivars, carry the rare S-allele S17, which had initially been described in wild sweet cherries in Belgium and Germany. The S17-allele in Estonian cultivars could originate from 'Leningradskaya tchernaya' (S6|S17), which has been extensively used in Estonian sweet cherry breeding. Four studied cultivars carrying S17 are partly self-compatible, whereas the other 20 cultivars with S17 have not been reported to be self-compatible. The recommended pollinator of seven self-incompatible sweet cherries is of the same S-genotype, including four with S17-allele, suggesting heritable reduced effectiveness of self-infertility. We classified the newly genotyped sweet cherry cultivars into 15 known incompatibility groups, and we proposed four new incompatibility groups, 64–67, for S-locus genotypes S3|S17, S4|S17, S5|S17, and S6|S17, respectively, which makes them excellent pollinators all across Europe. Alternatively, the frequency of S17 might be underestimated in Eastern European populations and some currently unidentified sweet cherry S-alleles might potentially be S17. [ABSTRACT FROM AUTHOR]