This chapter summarizes recent advances in sequencing and bioinformatics tools used to analyze commercially important aquatic species, particularly highlighting omics studies, key sequencing methods, assembly and analysis tools, and major insights. It also entails how genomics contributes to selective breeding, conservation, and evolutionary studies by identifying genetic markers and understanding adaptive traits. It also explores the role of proteomics in uncovering functional proteins, protein–protein interactions, and pathways important for fish growth, disease resistance, and environmental adaptation, supported by advances in protein databases and analytical techniques. The metabolomics section discusses strategies and methods for detecting and profiling metabolites to assess physiological states and responses to environmental changes. Finally, the chapter emphasizes the importance of multi-omics data integration using machine learning and computational approaches to unravel the complex biological networks governing aquaculture species, ultimately aiming to innovate sustainable practices and ensure aquatic food security.