Aquatic products, which are considered essential sources of protein, have received significant attention from both producers and consumers. Disease prevention and treatment in fish are, therefore, essential to guarantee the availability of healthy fish protein, in addition to ecological and economic benefits. Diagnostic methods for detecting pathogens in aquatic animals have improved from simple microscopic and morphological examinations to more sophisticated molecular methods. Molecular tools, in addition to traditional methods such as histology, microbiology, and immunology, enable the early detection of infectious diseases and, therefore, reduce mortality rates and losses in aquaculture production. Advances in molecular sequencing techniques have driven tremendous progress in biology, improving the diagnosis and management of pathogens through their study of complete genomes. These improvements in diagnostic methods have led to enhanced specificity, sensitivity, and speed and have been very critical in epidemiological research for identifying disease outbreaks that prevent infectious diseases from spreading further in aquaculture.