Bioinformatics is a scientific sub discipline that combines information technology, computer science and biology as a single discipline. Several bioinformatics applications accelerate biotechnological research, including genome sequencing, drug design, and protein structure and function analysis. Bioinformatics's role has reached its peak in various sectors, viz., genomics, proteomics, transcriptomics, cheminformatics, evolutionary studies, drug discovery, climate change studies, bioenergy/biofuels, crop improvement, forensic science, waste clean-up and biodefense. Analysis of any biological information is incomplete without software and statistics. Bioinformatics finds vast applications in aquaculture, especially in aquatic animal health management for disease diagnosis and drug or vaccine development; in nutrition for evaluating fish’s flesh quality and nutrigenomics and in desirable strain development for aquaculture. In fish pathology, Next Generation Sequencing enables the investigation of all relevant information in a single test related to molecular epidemiology, species identification, strain typing, virulence identification, pathogenesis mechanism and antimicrobial resistance. The transcriptomic studies reveal the effects of any pathogen or drug on the host by analyzing the gene expression. The proteomic analysis is helpful for drug target identification, drug design, protein-protein interaction, vaccine design, and more. Integrating multiple omics technology to obtain many outcomes of specific responses in certain living organisms is proliferating. Despite many applications of bioinformatics, challenges hinder its exponential use. Common challenges include data collection, storage, access, security, legal issues, and lack of knowledge about how the data is used, interpreted, and transferred. Yet it overcomes the time and money spent on tedious laboratory works in drug discovery, disease diagnosis and analysis of roles and effects of each gene or protein. A whole new era of personalized medicine will emerge from bioinformatics development.