Epigenetics is environmental modification of gene expression. These modifications do not alter genes; instead, they alter gene expression. In some cases, a gene is silenced; in others, it is enhanced. Some epigenetic changes to gene expression can be transmitted across generations, which means that it is non-genetic inheritance. Stable, heritable epigenetic changes are termed “epimutations.” Studies with fish show that various environmental parameters produce epimutations that affect many phenotypes, including growth, disease resistance, metabolism, behavior, and sex. Many epigenetic changes occur in the early generations of captive culture when a population is exposed to an environment that differs from the wild one. While epimutations can be beneficial in food fish aquaculture because they will increase the population’s hatchery fitness, these epimutations will be a liability in an aquaculture-assisted fisheries program because they will decrease fitness in the wild. This means that raising fish using traditional, intensive management in environmentally barren culture systems will produce epimutations that make the fish less fit in the wild and, when introgression occurs, these epimutations will be transferred to the wild population, lowing its fitness. The way to minimize the negative effects of epimutations in a cultured population of fish is to consider epigenetics and domestication to be conjoined twins. This means that undesired epimutations can be minimized by raising fish in an environment that mimics the wild and by using naturalized extensive management—conservation aquaculture.