Like all animals, fish are susceptible to many diseases and parasites. Parasitic infections are more commonly seen than microbial diseases. Research conducted in multiple fish disease diagnostic laboratories suggests that parasites make up 30 to 50 percent of all cases reported. Some of the parasites, however, cannot be distinguished from similar pathogens by traditional diagnostic techniques. Efforts have been undertaken to utilize biochemical tests, DNA homology analysis, and protease variability for identification. These methods, however, had limitations. They required the previous isolation of pathogens and failed to show adequate sensitivity for low levels of pathogens. Considerable advances over the past 15 years have occurred in understanding the molecular biology of fish pathogens as well as their hosts.Molecular techniques involving PCR, RT-PCR, LAMP, RFLP, RAPD, and AFLP, among others, are now used abundantly to support disease diagnosis improvement, control methods, and the epidemiological work of parasitic infections. DNA and RNA assays have been worthwhile in identifying microbes that cannot easily be cultured into the laboratory plates and in dead and living microbe identification, thereby contributing to creating new or modern diagnostic technologies. A better understanding of molecular tools for parasite detection can improve diagnostic accuracy, facilitate carrier identification, and support species discovery within various parasitic groups.