Japanese apricot (Prunus mume) originated in south-eastern China and is one of the major fruit trees in Japan. The major cultivars of Japanese apricot are self-incompatible. Self-incompatibility of Japanese apricot is gametophytic, the same as other Prunus species. Since S-genotype of every cultivar remained unclear until now, we examined molecular markers to determine S-genotype which was explored based on the information about S-RNase of other Prunus spiecies. Total DNA isolated from six cultivars was PCR-amplified by oligonucleotide primers designed from conserved region of Prunus S-RNase Every six cultivars yielded two amplified bands. In total, seven kind of polymorphism in molecular size were determined among those six cultivar, controlled pollination tests were carried out among cultivars that showed same band pattern, and these cross-combinations indicated cross-incompatibility. So, we were made clear that S-genotype of Japanese apricot could effectively and easily be determined by PCR method, and that there exists seven S-gene at least.