Gametophytic self-incompatibility (SI), an important character for breeding seedless cultivars of Citrus, is known in pummelo, mandarin, and many hybrid cultivars with pummelo in their pedigrees. Only a little is known about the allelic variation in the self-incompatibility gene (S), S allele frequencies, and the genotypes of self-incompatible and semi-self-compatible cultivars. In this study, pollination of 'Banpeiyu' S 1 seedlings with 'Banpeiyu' and pollination between the S 1 seedlings were performed to determine homozygous S 1 seedlings for the S gene. Seventyeight Citrus accessions, including 55 pummelo accessions, were pollinated with each of two homozygous S 1 seedlings (S 1 S 1 and S 2 S 2 ). Pollen tube arrest in the style base of their pollinated pistils indicated that 23 accessions, including 'Banpeiyu', have an S 1 allele each and 16 accessions, including 'Banpeiyu', have an S 2 allele each. Frequency of accessions with S 1 allele was 29.9% (23 of 77 accessions examined) and S 1 allele frequency was 16.4% (23 of 140 alleles excluding S f allele). Frequency of accessions with S 2 allele was 21.3% (16 of 75 accessions examined) and S 2 allele frequency was 11.6% (16 of 138 alleles excluding S f allele). Pummelo accessions collected from Kagoshima Prefecture had S 1 alleles with two and half times higher frequency (56.3%) than that in all accessions examined. Of the 79 accessions, six accessions ('Banpeiyu', 'Iriki Buntan', 'Kaopang', Nagashima Buntan No. 6, Nagashima Buntan No. 7, and 'Soyu') were S 1 S 2 genotypes. The Citrus cultivars, whose S genotypes have been fully determined in this study, were