Aquaculture plays a critical role in global food security by providing affordable, high-quality protein and supporting several UN Sustainable Development Goals. Its growth, however, faces major challenges, including disease outbreaks, climate change impacts, reliance on unsustainable feed resources, and environmental concerns. Emerging omics technologies such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, and metagenomics are revolutionizing aquaculture by enabling advanced selective breeding, precise disease diagnostics, sustainable feed innovation, and the development of climate-resilient strains. The integration of multi-omics with cutting-edge tools like bioinformatics, artificial intelligence, and high-throughput sequencing is driving a shift toward intelligent aquaculture systems that merge biological and environmental data for real-time decision-making. Coupling omics with digital innovations such as IoT, big data analytics, and blockchain strengthens traceability, production efficiency, and sustainability. Despite hurdles like high costs, limited infrastructure, and regulatory gaps, the convergence of omics and precision technologies offers transformative opportunities. These innovations have the potential to make aquaculture a cornerstone of the blue economy, ensuring resilient, efficient, and sustainable production systems to meet the growing global demand for safe and nutritious aquatic foods.