Bioinformatics has become integral across diverse fields such as agriculture, medicine, engineering, life sciences, evolutionary biology, drug discovery, climate studies, biofuels, crop improvement, forensics, waste management, and biodefense. The analysis of biological data today is inseparable from computational tools and statistics. In aquaculture, bioinformatics plays a critical role in aquatic animal health for disease diagnosis, vaccine and drug development; in nutrition for assessing flesh quality and nutrigenomics; and in selective breeding for strain improvement. Next Generation Sequencing allows comprehensive analysis in a single test, covering molecular epidemiology, species identification, strain typing, virulence, pathogenesis, and antimicrobial resistance. Transcriptomics helps assess host responses to pathogens or drugs via gene expression analysis, while proteomics aids in identifying drug targets, protein interactions, and vaccine design. The integration of multi-omics technologies is rapidly expanding. Despite its wide applications, challenges such as data management, legal concerns, and skill gaps persist. Nonetheless, bioinformatics significantly reduces time and cost compared to traditional lab-based approaches in disease diagnostics and functional genomics. This chapter offers an in-depth overview of bioinformatics advancements and their applications in aquatic animal health management with emphasis on the use of omics technologies. The integration of computational tools with biological data is transforming aquaculture health management, making it more precise, efficient, and sustainable.