Aquaculture is a rapidly growing food production system that plays an essential role in achieving nutritional security. Traditional aquafeed formulation approaches overlook the complex relationships between diet, physiology, and environment, as well as species-specific nutritional requirements. To overcome these challenges, scientists, researchers, and aquaculture experts are focusing on developing new technologies to support sustainable aquaculture and improve food and nutritional security. Our understanding of aquatic organisms at the molecular level has been completely transformed in recent years by the introduction of advanced omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, and nutrigenomics. These technologies have also provided new tools to improve nutritional strategies in aquaculture. Genomic technologies make it easier to identify genetic markers associated with food metabolism and feed efficiency. Transcriptomic analyses help in modifying feed compositions to optimize metabolic outcomes by revealing patterns of gene expression under various dietary regimes. Proteomics and metabolomics investigate dynamic responses to dietary inputs by examining protein functions and metabolic pathways, facilitating the identification of bioactive substances and nutrient markers. Epigenomic research indicates that an early-life diet can cause heritable changes in gene expression, suggesting the possibility of nutritional programming. Nutrigenomics is an integrative approach that explains host-diet interactions and allows the development of species-specific diets for optimal performance. This chapter addresses the existing situation, recent advancements, and future possibilities of omics technology for maintaining nutritional security in aquaculture. These innovations will open the door to sustainable food production systems, which promote human nutrition and environmental resilience.