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Bioinformatics is one of the ongoing trends of biological research integrating gene based information and computational technology to produce new knowledge. It works to synthesize complex biological information from multiomics data (results of high throughput technologies) by employing a number of bioinformatics tools (software). User convenience and availability are the determining factors of these tools being widely used in bioinformatics research. BLAST, FASTA (FAST-All), EMBOSS, ClustalW, RasMol and Protein Explorer, Cn3D, Swiss PDB viewer, Hex, Vega, Bioeditor etc. are commonly operated bioinformatics software tools in fisheries and aquaculture research. By default, these software tools mine and analyze a vast biological data set using the available databases. However, aquaculture scientists can use bioinformatics for genomic data manipulation, genome annotation and expression profiling, molecular folding, modeling, and design as well as generating biological network and system biology. Therefore, they can contribute in specified fields of aquaculture such as disease diagnosis and aquatic health management, fish nutritional aspects and culture-able strain development. Although having huge prospects, Bangladesh is still in infancy of applying bioinformatics in aquaculture research with limited resources. Research council at national level should be formed to bring all the enthusiastic scientists and skilled manpower under a single umbrella and facilitate to contribute in a collaborative platform. Besides, fully-fledged bioinformatics degree should be launched at University levels to produce knowledgeable and trained work force for future research. This review was attempted to shed light on bioinformatics, as young integrated field of bio-computational research, and its significance in aquaculture research of Bangladesh.