Summary The inheritance of self-compatibility conferred by the Se-haplotype in Japanese plum (Prunus salicina Lindl.) was investigated in various progeny. Only those progeny with the Se-RNase allele set fruit after self-pollination, indicating that self-compatibility conferred by the Se-haplotype was inherited in these progeny (i.e., the Se-haplotype co-segregated with self-compatibility). In addition, Se-RNase allele-specific PCR primers were developed, since detection of the Se-RNase allele using S-RNase consensus primers was time-consuming and not always reliable. PCR using the primer pair Se-Fw1-Plum and Se-Rv1-Plum, designed from a sequence in the second intron of the Se-RNase gene, resulted in a fragment present only in those cultivars and seedlings having the Se-haplotype. Thus, this primer pair specifically amplified the Se-RNase gene. These results suggest that PCR using this primer pair can be used for the early selection of self-compatible offspring with the Se-haplotype when breeding Japanese plum.