There are several pairs of similar class I S haplotypes between Brassica oleracea and Brassica rapa. The similar S halotypes in these interspecific pairs have been reported to have the same recognition specificities. In the present study, three interspecific pairs showing a high sequence similarity were found in class II S haplotypes, i.e. between BoS-2b (B. oleracea S-2b) and BrS-44 (B. rapa S-44), between BoS-5 and BrS-40, and between BoS-15 and BrS-60. By pollination tests using interspecific hybrids between B. oleracea and B. rapa, BoS-5 and BoS-2b were revealed to have slightly and completely different recognition specificities from those of BrS-40 and BrS-44, respectively. The recognition reaction between SP11 and SRK of BoS-15 was suggested to be incomplete. The regions of class II SP11 and SRK important for self-recognition specificity and the diversification of class II S haplotypes are discussed herein.