Traditionally, the diagnosis of infectious diseases has been accomplished by the isolation of the infecting microorganism in pure culture. Classical methods of microbial isolation and identification have been invaluable in the study of bacterial, viral and fungal infections. However, cultivation systems offer disadvantages for the rapid diagnosis of infectious diseases. For example, many microorganisms, especially viruses and slow growing bacteria, require a considerable period of time in cultivation that the results from cultures are often not available at a time when the result can alter the course of therapy. Thus, more sensitive means must be applied for detecting and identifying a wide range of infectious diseases of fish and shrimps. The development of rapid, simple, sensitive and specific diagnostic tests for infectious diseases has been much slower than the other disciplines of medicine. This is partially attributed to the complexity and diversity of the pathogenic organisms and to the difficulty in detecting low concentrations of these organisms in samples. Immunological and molecular biology-based techniques are rapidly advancing the field of diagnostics in fish and shrimp diseases.