Egypt is the world’s ninth-largest fish producer with a total production of 1.5 billion tons per year, and farmed fishes comprise almost 79.6% of the total production. Massive mortalities in market-sized farmed fish (freshwater and marine species) were documented all over fish farms in Egypt leading to serious economic losses. The poor biosecurity practices and awareness among smallholder fish farmers accompanied with a long period of temperature fluctuation may predispose farmed fish to be simultaneously coinfected with multiple pathogens. Moribund fishes usually exhibited various septicemic clinical signs and post-mortem lesions indicating that one or more septicemic bacterial pathogens were involved in these outbreak reports. Therefore, rapid and accurate identification of pathogens in the asymptomatic fish population is important for preventing the occurrence of infectious diseases and protecting consumers from seafood-borne illnesses. Molecular techniques provide sensitive, quick, and accurate data for identifying specific pathogens without the need for time-consuming traditional techniques. In addition, the development of cost-effective molecular techniques facilitates their wide implementation in routine clinical diagnostic approaches. Molecular diagnostic methods are useful for simultaneously identifying multiple bacterial pathogens that were challenging to recognize by commercial biochemical techniques. Genetic testing procedures could determine the genetic diversity between closely related strains at the subspecies level. Consequently, these techniques are required for the development of detecting methods for specific strains and for epidemiological investigations in bacterial diseases. This review documented a variety of molecular techniques, including amplification of nucleic acids, polymerase chain reaction (PCR), nested PCR, real-time PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP), DNA microarrays, and nucleotide sequencing assays, that are commonly used to identify fish pathogens.