For much of the twentieth century, it was accepted that genes dictate phenotypes. Nevertheless, genetics in combination with molecular biology and genomics has facilitated the explanation of some peculiar molecular phenomena. Most eukaryotic genomes are crammed with noncoding DNA, which was previously hypothesized to be selfish DNA, with only a small fraction of sequences encoding proteins. We now know that the genes are not blueprint for phenotypes. Typically, genes interact with the environment to form phenotypes. Epigenetic regulation modifies genes. Epigenetics is defined as a "stably heritable phenotype resulting from changes in chromosomes without alterations to DNA sequences". The theme of this special issue is "Genomic perspectives on epigenetics." Here, we review 12 articles that reflect considerable advancements in this rapidly evolving subject area.