Epigenetics, the study of heritable changes in gene expression that do not involve alterations in the DNA sequence, has garnered increasing attention in the field of fisheries and aquaculture. Environmental factors such as climate change, pollution, and nutritional shifts can influence gene activity through mechanisms like DNA methylation, histone modifications, and noncoding RNAs. These epigenetic changes play a critical role in shaping traits such as growth, disease resistance, stress tolerance, and sex determination in aquatic species. The application of epigenetics holds significant promise for enhancing aquaculture productivity and sustainability by improving stress resilience, optimizing nutrition, and increasing disease resistance, thereby reducing the reliance on antibiotics and enhancing food security. Epigenetic inheritance, especially in aquatic species with less extensive embryonic reprogramming, presents opportunities for transgenerational adaptation to environmental challenges. Despite its potential, research in epigenetics within aquaculture remains in its early phase, with significant gaps in understanding the interaction between genetic and epigenetic factors. This chapter highlights key advancements in epigenetic research for fisheries, discusses the potential applications of epigenetics in sustainable aquaculture, and outlines future research directions needed to integrate epigenetic insights into breeding programs and aquaculture management strategies.