Self-compatible cultivars of Japanese apricot (Prunus mume Sieb. et Zucc.) have a common S-RNase (S-f-RNase) gene that can be used as a molecular marker for self-compatibility. In this study, we further characterized S-f-RNase by comparing S-7-RNases of self-compatible 'Kensaki') and self-incompatible 'Nankou' (S-1 S-7). cDNA libraries from the styles with stigmas of these two cultivars were constructed and cDNAs encoding S-f-, S-1-, and S-7-RNases were cloned. Deduced amino acid sequences from these cDNAs all contained two active domains of the T2/S type RNase family and five conserved regions of the rosaceous S- RNase. RNA blot analysis showed that the S-f-, S-1-, and S-7-RNase genes were transcribed in the pistil but not in the leaf as with other S-RNase genes of Prunus. Furthermore, 2D-PAGE analysis revealed that S-f-RNase has molecular mass, isoelectric point, and immunological characteristics similar to other S-RNase. These results indicate that the pollen -S gene that is supposedly tightly linked to the S-f-RNase gene may be responsible for the self-compatibility observed in the S-f-haplotype.