In aquatic ecosystems, pathogen exposure to native hosts is a continuous and ubiquitous issue, maybe even more so than in terrestrial systems. Microorganisms that can cause harm to the host are referred to as infectious pathogens. One of the biggest dangers to aquaculture's development is infectious diseases. The care of several fishes crammed into a tiny area provides the perfect environment for the development and spread of infectious diseases. In this crowded, artificial environment, fish are more prone to illness. Furthermore, due to the aquatic environment and constrained water flow, diseases spread more quickly in densely populated areas. However, the rapid development of molecular biology techniques has been one of the most remarkable trends in recent years in the biological sciences. Nowadays, the theory and technology of molecular biology are widely used in fields such as the development of plants and animals, the diagnosis and treatment of human diseases, and others. Approaches from molecular biology are now being employed in extremely valuable aquatic habitats. In order to advance aquaculture technology, expand into new areas, and alter the dominant industrial paradigm, molecular biology is essential. Depending on the scope and goal of the research, molecular biology techniques can be employed to identify dangerous bacteria down to sub-species or strains. Examples of molecular diagnostic techniques include polymerase chain reaction (PCR), probe hybridization, restriction enzyme digestion, and nucleotide sequencing. The first two being most frequently employed. Fish, shrimp, and shellfish have all been successfully tested for bacterial, viral, parasitic, and fungal infections using molecular diagnostic technology.

Many countries have investigated and examined molecular biology techniques connected to aquaculture, with a focus on creating new kinds of superior breeding, raising high-yield, stress-resistant types, and creating new technologies and ways for diagnosing and treating illnesses. In order to improve aquaculture species and prevent disease, molecular biology approaches still have a lot of potential for development. Enzymatic synthesis and amplification of specific DNA fragments in vitro is known as PCR. One of the most popular molecular detection techniques is it. A typical reaction system includes templates, primers, polymerase, deoxynucleoside triphosphate, and the required buffer. In the PCR thermal cycle, denaturation, annealing, and extension all take place. The need for additional verification tests arises from the fact that the PCR is affected by a number of different factors (such as restriction enzyme digestion, probe hybridization, or nucleotide sequencing). A lot of researchers have created numerous PCR-based pathogen detection methods. For instance, the fstA gene was amplified by PCR to identify Aeromonas in salmon, and a multi-PCR was created to simultaneously detect five different bacterial diseases in fish. A nested PCR was used to find the Penaeus monodon White Spot Syndrome Virus (WSSV).

According to the base pairing theory, in situ nucleic acid hybridization creates hybrids by binding recognised base sequences with designated nucleic acid probes and nucleic acid bases in structures or cells. The histochemistry or immunohistochemistry staining processes are used in conjunction with the matching markers detecting equipment to create the hybridization signals with a colour in situ. This strategy makes use of PCR technology, as well as the benefits and drawbacks of each group. Immune PCR has a high sensitivity, with antigen material mass concentrations as low as 2 ng/L. Investigating the situation was crucial because there were many factors that affected it. Real-time quantitative fluorescence PCR Specificity effectively eliminates PCR contamination despite nested-PCR's 100 times greater sensitivity than standard PCR, quick complexity in operation, and propensity to pollute the environment. Hybridization, for instance, was utilised to detect WSSV in Chinese shrimp, illustrating the broad variety of uses for this method in the detection of outbreaks of shrimp epidemics. The gyrase B gene (gyrB) was employed as a molecular diagnostic probe.