The dynamic interplay between environment, diet, and gene regulation in aquatic organisms is increasingly being understood through the lens of epigenetics. This chapter explores the molecular epigenetic mechanisms—DNA methylation, histone modifications, and noncoding RNAs that enable aquatic species to adapt to their surroundings without changes to their DNA sequence. These epigenetic processes orchestrate gene expression patterns in response to external stimuli such as temperature, salinity, pollutants, and nutritional inputs, especially during sensitive early developmental stages. In recent years, scientific studies have revealed that these environmentally induced epigenetic changes can influence critical physiological traits in fish and shellfish, including growth rates, immune function, metabolism, reproductive success, and stress resilience. In particular, diet or nutrition plays a significant in shaping the epigenome of aquaculture species. The transition to plant-based feeds, early-life nutritional programming, and micronutrient supplementation have been shown to trigger heritable epigenetic modifications affecting metabolic efficiency and health outcomes. Simultaneously, environmental stressors such as thermal fluctuations and water quality can induce reversible or transgenerational epigenetic responses that impact sex determination, disease resistance, and overall fitness. By integrating findings from recent research, this chapter discusses the implications of these epigenetic mechanisms for aquaculture development. It highlights how understanding and leveraging these biological processes can lead to more sustainable and adaptive farming practices. While challenges remain, particularly regarding species-specific epigenomic data and long-term validation, epigenetics is emerging as a critical frontier in advancing precision aquaculture. This chapter aims to provide a comprehensive overview of how “epigenetic waves” driven by environment and diet can be harnessed to shape the future of global aquaculture.