The integration of omics technologies—genomics, transcriptomics, proteomics, metabolomics, and nutrigenomics—is revolutionizing aquaculture nutrition by enabling precise insights into nutrient–gene interactions, metabolic pathways, and host–microbiome dynamics. These approaches allow the identification of novel feed ingredients, optimization of nutrient utilization, and development of species-specific diets that enhance growth, immunity, and stress tolerance. Omics-driven strategies also facilitate the reduction of fishmeal and fish oil dependency by supporting the effective use of sustainable alternatives such as plant-based proteins, insect meals, and algal biomasses. Moreover, advanced bioinformatics and machine learning tools are enhancing data integration, leading to predictive models for nutrient requirements and health outcomes. The future of aquaculture nutrition lies in personalized, environmentally sustainable feeding strategies guided by omics insights, ultimately improving production efficiency and global food security. By bridging molecular biology with nutrition science, omics will define the next frontier in sustainable aquaculture.