This study aimed to identify anatomopathological injuries in sick, moribund, or recently dead fish from an experimental fish farm in the Peruvian Amazonia with a necropsy, direct microscopic, and histopathological examination. The study was carried out at the migratory fish production unit where cachama (Colossoma macropomum), pacus (Piaractus brachypomus), black prochilodus (Prochilodus nigricans), and spotted tiger shovelnose catfish (Pseudoplatystoma punctifer) are bred. Furthermore, from the non-migratory fish unit where arapaima (Arapaima gigas) and Nile tilapia (Oreochromis niloticus) are bred at the fish farm within the Experimental Station of the IVITA Research Center in Ucayali, Peru. Thirty clinical cases distributed in thirteen incidents of diseases observed between January 2013 and June 2014 were evaluated. The tissue macroscopic and microscopic evaluations were performed through necropsies to determine the injuries and the possible causes of mortality. Samples of the skin and gills mucous membrane were collected to identify parasites by direct microscopy, and liver, kidney, and spleen imprints stained with Gram were made to observe the presence of bacteria. Histopathological analyzes of the affected tissues were also performed in some of the evaluated cases. Parasites, mainly trematodes, were found in cachama, protozoa in arapaima, and bacteria suggestive of Flavobacterium sp. in spotted tiger shovelnose catfish. Digestive (14/30), respiratory (9/30), and traumatic (3/30) injuries were identified.