Parasitology today focused on studying parasites infecting fish. Parasitic infestation is one of the most important problems facing fish breeding and production. All fish carry pathogens and parasites. Among fish parasites, especially ectoparasites, protozoa occupy a very important and dangerous group that causes severe economic losses and mortalities in freshwater pisciculture. Also, monogenetic trematodes of freshwater fishes could be considered as one of the most prevalent diseases affecting skin and gills, which included irritation, severe destruction of the gills, impaired breathing as well as severe losses too.the present study aimed to investigate the incidence, identification and morphological description of some protozoan parasites and monogenetic trematodes infecting different fresh water fish species collected from two different ecosystems along the River Nile in Egypt, the first ecosystem represented by a location at Giza province, and the Pharonic Sea located at Menoufia province represented the other ecosystem. This study depended on light and transmission electron microscopy.