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, a heritable epigenetic modification, in which the modification is attributable to the degree of methylation of a gene and not to the change in its sequence, sometimes occurs and can affect the level of gene expression by reducing its transcriptional level. Some examples of epigenetic phenomena mediated by allele-specific DNA methylation in plants found to date include genomic imprinting, nucleolar dominance, and paramutation. Unlike the case in mammals, epigenetic modifications of plant genes are thought to be mitotically and meiotically stable, but recent studies of allele-specific demethylation at the FWA and MEDEA loci and recessive allele-specific methylation of Brassica self-incompatibility alleles indicate that DNA methylation patterns in plants can vary temporally and spatially in each generation. In this review, we describe various epigenetic phenomena regulated by allele-specific DNA methylation and their possible underlying mechanisms.