Over time, aquatic pathology has gained awareness and relevance worldwide due to the expansion of aquaculture and the effects of climate change. A key component of health management is an accurate disease diagnosis. The entire farmed fish population may go extinct as a result of late detection of fish diseases. There are various methods for conducting research on the health status of aquatic animals. In addition to improving production yields and helping to diagnose and avoid diseases, histology can also be used to identify potential signs of microbial pathogens or environmental contamination through changes in cellular structure. In order to maintain tissue and cell structure as quickly as possible in their in vivo condition, proper fixation is essential. The ideal and suggested ratio between tissue and fixative volume should be 1:10. Dead fish should never be collected to prevent misunderstandings caused by autolytic changes. Only living, moribund, or impaired fish should be chosen for fixation and histological analysis. To allow the fixative medium to quickly enter the tissue and assure appropriate fixation quality, the sample size should have a maximum area of 5 × 10 mm and a maximum thickness of 5 mm. In addition to providing the most popular histological examination methods to researchers and fish farmers, the writers of this chapter would like to highlight the primary changes linked to various fish organs.