This report demonstrates the diversity of S-haplotypes in Japanese plum by molecular, cloning of genomic DNAs and cDNAs that encode S-RNases. Nine different DNA fragments, designated as S-S', were obtained from 17 Japanese plum cultivars by PCR with an S-RNase gene-specific primer set, Pru-C2 and PCE-R. Eleven different S-haplotypes were found in these cultivars. The banding patterns obtained with another S-RNase gene-specific primer set, Pru-T2 and PCE-R, corresponded to the S-haplotypes predicted from the Pru-C2 and PCE-R primer set. Several cultivars had the same S-haplotypes. Partial genomic DNAs for eight S-RNase genes and cDNAs for two S-RNases were cloned and sequenced. Deduced amino acid sequences contained conserved regions among the rosaceous S-RNases. Comparisons of the-sequences from cDNAs and genomic DNAs revealed the presence of two introns in the S-RNase genes of Japanese plum as in other Prunus S-RNase genes. Pollination incompatibility groups and self-compatibility in Japanese plum were discussed with reference to the S-haplotypes.