Japanese pear (Pyrus pyrifolia Nakai), a member of the Rosaceae, shows gametophytic self-incompatibility that is controlled by the S-locus. The S-genotype of Japanese pear cultivars is an important factor for crossing and breeding. We report a rapid reliable method to identify these S-genotypes. It consists of PCR amplification of the S-RNase gene from genomic DNA and subsequent digestion of the PCR fragments with S-allele-specific restriction endonucleases. Using this method, we determined the unknown S-genotypes of nine Japanese pear cultivars and selected self-compatible varieties from the offspring of the self-compatible cultivar, ‘Osa-Nijisseiki’.