The aquatic epigenome refers to the genetic modifications in aquatic organisms that do not alter the DNA sequence but affect gene expression. Environmental factors such as temperature, pollutants, and diet can influence epigenetic changes, impacting the growth, reproduction, and disease resistance of aquatic species. In aquaculture, understanding the aquatic epigenome can improve breeding programs and enhance farmed species' ability to adapt to varying environmental conditions. Research in this area allows for more sustainable and efficient farming practices by selecting for traits that increase resilience and productivity while reducing the impact of diseases and environmental stressors. Advances in epigenetic research offer potential solutions for improving aquaculture’s adaptability in the face of climate change.