Nutrigenomics is a multidisciplinary research field in aquaculture that provides valuable insights into the interaction between nutrients and the genome to improve the health, growth, and sustainability of aquaculture species. The advancement of high-throughput technologies like transcriptomics, proteomics, metabolomics, and epigenomics has greatly enhanced the knowledge of nutrient-gene interactions. These technologies provide important information on metabolic control, immune processes, growth mechanisms, and dietary adaptations in aquatic species. Genomic information facilitates the identification of genetic differences impacting nutrient metabolism, while transcriptomics identifies gene expression differences under varied diets. Proteomics offers direct evidence of nutrition-affected functional proteins, and metabolomics reveals metabolic signatures associated with feed efficiency and health. Epigenomics sheds further light on environmental and dietary induction of heritable gene regulation changes that underlie stress adaptation, sex determination, and metabolic programming. In microbiomics, although substantial progress has been made, it is still underutilized in aquaculture nutrition due to species-specific microbiota heterogeneity and technical limitations. Recent omics technology like single-cell sequencing holds the potential for determining cell-specific dietary impacts and nutrient-responsive pathways. The convergence of multi-omics strategies facilitates the shift toward precision nutrition, allowing for customized diet formulation for optimized performance, disease resistance, and environmental sustainability. This chapter gives an integrative review of nutrigenomics and its evolution, current applications, and potential for the future in aquaculture. Additionally, it positions nutrigenomics as a revolutionary framework that connects molecular information and functional aquaculture outcomes, ultimately leading to resilient, productive, and eco-friendly aquaculture systems.