Common buckwheat plants have heteromorphic self-incompatibility. Using two self-fertilizing lines, we revealed that there are two distinct systems of self-compatibility, one using a self-compatible allele, S^h, the other using modifier genes located outside the S locus and suppressing the functions of the S-locus genes. S^h appears to have been produced by recombination in the S supergene (gi^SI^PPA/gi^SI^PPA), in which each gene is functional. The modifier genes control the intensity of self-incompatibility and have three distinctive features: (1) Pollen shows cross-compatibility with styles of all flower types, although the compatibility is influenced by the genetic background of those plants. (2) Flower morphology of F₁ plants is controlled by the genotype of the S locus. (3) F₁ plants show high self-compatibility, although the level of self-compatibility is influenced by genetic background. The use of these genes for buckwheat breeding is discussed.