This chapter aims to provide an overview of epigenetic machinery present in fishes and provide examples of how epigenetics can have functional consequences under a variety of biotic and abiotic stimuli through both laboratory and naturally invoked experimental approaches. The mechanisms driving epigenetic change that have been studied most extensively in the fish literature are changes in DNA methylation, histone modification, and the effects of non-coding RNA. Temperature plays a major role in fish physiology. With the looming threat of predicted increases in freshwater and marine surface temperatures, it becomes essential to understand the epigenetic factors that affect the plastic response of fishes to warming waters, driving the ability of fish to cope with and respond to a changing global climate. In particular, the majority of research has focused on two main avenues of epigenetic mechanisms that drive adverse phenotypic outcomes: DNA methylation and miRNA.