Microbiology is one of the important areas in the aquaculture due to its beneficial as well as harmful effects to the fish or shrimp. Microorganisms are including bacteria, virus, fungus, protozoa, parasites, algae, etc. Among these, the major concern are bacteria and virus; however, most of the fish diseases are caused due to bacteria; and most of the shrimp diseases are caused due to virus. In bacterial concept, the beneficial species are considered as probiotics. Our established microbiology unit mainly focused in identifying different microbes which are causing diseases in the aquaculture organisms; and the identified microbes are completely characterised at molecular level to address the infection. The molecular studies on such microbes leads us to develop disease control strategies and then product formulation or technology development. Hence, the unit was established in such a sophisticated way with necessary instrumentation facilities.