Sour cherry is a tetraploid species, and gametophytic self-incompatibility (SI) operates in this species in the same way as in other stone fruit trees. However, while self-compatibility is most common in sour cherry and self-compatibility (SC) genotypes are rarely found, both SI and self-compatible (SC) types are selected in sour cherry. In this work, S-alleles have been identified for 70 sour cherry accessions and cultivars from the Shabestar regions of Iran, with S-genotypes of 68 cultivars identified for the first time. To identify the S-alleles, PCR-based methods were used. The amplification of the different alleles using combinations of the four forward primers (PaConsI-F, PruC2, PaConsII-F, EM-PC2consFD) and the five reverse primers (PruC4R, PCE-R, PaConsI-Rnew, PaConsII-R, EM-PC5consRD) revealed that they were the most useful for the identification of the sour cherry alleles. Nine known S-haplotypes (S6, S4, S9, S6m, S6m2, S24, S26, S35, S36a) were identified. In our study, alleles S6, S9, and S6m2 had a high frequency. It was shown that the consensus primers can be used to detect incompatibility alleles in sour cherry accessions. Our study has proved that the diversity of S alleles between the studied accessions was low, indicating low genetic diversity, which could also be due to the selection of superior genotypes by farmers.