Self-incompatibility system has been most intensively studied in Brassica because of the advantage as plant materials and the importance as crop species. The determinants of self-recognition specificity in the stigma and the pollen are SRK and SP11/SCR, respectively. The genes of SRK and SP11 have many alleles in a species and are closely linked with each other in the S-locus complex. A set of SRK and SP11 alleles are referred to as S haplotype. Sequence analyses of many alleles of SRK and SP11 in Brassica species revealed pairs of S haplotypes having highly similar SRK and SP11 alleles between different species. The interspecific pair of S haplotypes is considered to be derived from the same ancestral S haplotype and to have maintained the same recognition specificity. The structure of the S-locus complex is highly variable, and this high structural polymorphism is considered to be important for suppressing the recombination between SRK and SP11, which may result in the breakdown of self-incompatibility. The first candidate protein identified as the female S determinant was SLG, which is abundant on the stigma surface, but the function of SLG in self-incompatibility is unclear. The dominance relationships of the SRK alleles are different from those of the SP11 alleles, and dominance order of S haplotypes is nonlinear. Recently, methylation of the promoter region of SP11 has been reported to be responsible for transcriptional suppression of recessive SP11. Several mutations in SP11 and SRK causing self-compatibility have been identified, and other genes controlling self-incompatibility have also been reported. These molecular studies can contribute to the development of the F1 hybrid breeding using the self-incompatibility system in Brassica crops.