Cross-incompatible combinations among the main cultivars in apple are rarely reported in Japan. Recently, however, most new Japanese cultivars are progenies of `Ralls Janet', `Delicious', `Golden Delicious', `Jonathan', and `Indo'. Cross incompatibility in apple, therefore, will become a serious problem in the near future. Since the analysis of the S-allele genotypes were not performed, especially in Japanese apple cultivars, the fruit set percentage were examined in several combinations of `Hatsuaki' (`Jonathan' × `Golden Delicious') and `Iwakami' (`Fuji' × `Jonathan') progenies using back crossings. As a result, we found that `Golden Delicious' and `Jonathan' had no common S-allele, while `Fuji' and `Jonathan' had one common S-allele. These facts were used as basics for the S-allele genotype analysis, and fruit set percentage and seed number per fruit were investigated on a large scale. The cross seedlings between `Delicious' and `Jonathan', `Ralls Janet' and `Jonathan', `Iwakami' and `Golden Delicious', `Golden Delicious' and `Delicious', `Hatsuaki' and `Fuji', `Hatsuaki' and `Delicious', `Hatsuaki' and `Jonathan', and `Hatsuaki' and `Golden Delicious' were analyzed. In addition, incompatibility between `Redgold' and `Kinesei' (`Golden Delicious' × `Ralls Janet'), `Senshu' (`Toukou' × `Fuji') and `Iwakami', and progenies of `Northern Spy' also were analyzed. As a result, we have found the existence of six alleles and 15 genotypes, and we have established S-allele standard cultivars and strains as follows: (Sa, Sb) = `Golden Delicious'; (Sa, Sc) (4)-354, (4)-425; (Sa, Sd) = `Toukou'; (Sa, Se) = `Redgold', `Kinsei'; (Sa, Sf) = `Narihokou', (4)-4195; (Sb, Sc) = `Hatsuaki', `Kuifua', `Sekaiichi'; (Sb, Sd) = `Tsugaru', (4)-300; (Sb, Se) = (4)-150, (4)-743; (Sb, Sf) = `Northern Spy', M.9, `Umezawa'; (Sc, Sd) = `Jonathan', `Himekami'; (Sc, Sf) = `Fuji', `Shinkou'; (Sd, Se) =; (Sd, Sf) = `Senshu', `Iwakami'; (Se, Sf) = `Ralls Janet'.