In sour cherry, as in other species of the genus Prunus, there is a gametophytic self-incompatibility (GSI) phenomenon. In this research, relations between pollen and pistil of 10 superior sour cherry genotype were investigated by using biological and molecular methods. In biological methods, pollen grains are prepared in balloon stage (D phenological stage) and then after evaluating the growth and percentage of pollen germination in medium, in suitable time flowers were emasculated, open pollination, controlled self and cross pollination were carried out in the orchard. In the molecular method, PCR-based methods were used to identify S alleles. The results showed that the highest pollen germination was observed on the stigma in self-pollination, and regarding of the number of pollen tube at the upper and lower parts of the pistil and ovary, the highest was related to open pollinating. Nine known S-haplotypes (S4, S6, S9, S6m2, S24, S26, S35, S36b and S36a) were identified, that alleles S6/S6m2, S9, S24 have a high frequency. Our study showed the low diversity of S alleles between studied genotypes. According to the growth of pollen tubes in style and ovary in all cases of pollination all of studied genotypes are compatible.