Recent advances in technical innovations for DNA sequencing and their expression array analyses have accelerated understanding of mechanisms for gene regulation in diverse organisms from prokaryotes to eukaryotes including plants. During analyses of these data, it has become clear that heritable epigenetic modifications, in which the modifications are attributed to the degree of methylation of a gene and not to the change in its sequence, sometimes occur and can affect the level of gene expression by reducing its transcriptional level. DNA methylation at cytosine residues has been found to affect many important biological processes, including maintenance of genome integrity, developmental regulation, and regulation of gene expression. In many organisms, allelic diversity generates phenotypic variations and contributes to many events, such as development, adaptation to changing environment, and genome evolution. Allelic diversity is generally defined by the difference in nucleotide sequences that code for a gene. However, recent studies on recessive allele-specific DNA methylation of Brassica self-incompatibility alleles demonstrate that DNA methylation patterns in plants can vary temporally and spatially in each generation. In this review, we firstly present overview of self-incompatibility system in Brassica and then describe dominance relationships in Brassica self-incompatibility regulated by allele-specific DNA methylation and their possible underlying mechanisms.