Most commercial cultivars of japanese plum (Prunus salicina Lindl.) exhibit S-RNase-based gametophytic self-incompatibility (GSI), although some self-compatible (SC) cultivars exist. In this study, we characterized S-RNase and SFB, the pistil and pollen S determinants of the specificity of the GSI reaction, respectively, from four S-haplotypes, including a SC (S-e) and three SI (S-a, S-b, and S-c) S-haplotypes of japanese plum. The genomic organization and structure of the SC S-e-haplotype appear intact, because the relative transcriptional orientation of its S-RNase and SFB and their intergenetic distance are similar to those of the other three SI S-haplotypes of japanese plum and other Primus L. species. Furthermore, there is no apparent defect in the DNA sequences of S-e-RNase and SFBe. However, a series of transcriptional analyses, including real-time reverse transcriptase-polymerase chain reaction, showed that the S-e-RNase transcript levels in the pistil are significantly lower than those of the S-a-, S-b-, and S-c-RNases, although transcripts of SFBa, SFBb, SFBc, and SFBe are present at similar levels in pollen. Furthermore, no S-e-RNase spot was detected in two-dimensional polyacrylamide gel electrophoresis profiles of stylar extracts of the cultivars with the S-e-haplotype. We discuss the possible molecular basis of SC observed with the S-e-haplotype with special reference to the insufficient S-e-RNase accumulation incited by the very low transcriptional level of S-e-RNase in pistils.