The present study was carried out on three freshwater fishes Oreochromis niloticus (wild and cultured), Clarias gariepinus and Lates niloticus which were collected from different localities from February to November (2013). The infested fishes showed no pathognomonic clinical signs except slight abdominal distention. Fish species subjected to parasitological revealed presence of encysted metacercaeiae which including (Clinostomum spp, Euclinostomum spp, Haplorchid, Cyanodiplostimatid and Prohemistomatide). Nematodes are including (Procamallanas laeviconchus, Paracamallanas cyathopharynx and contracaecum spps), Cestodes including Polyonchobothrium clarias and Acanthocephalan including Acanthocentis tilapiae and Neoechinorhychus rutilli. The highest seasonal prevalence of internal parasites was found in spring followed by summer then autumn and winter also the highest prevalence of the isolated parasites was observed in Lates niloticus followed by Clarias gariepinus then wild Oreochromis niloticus and cultured ones. The PCR amplification of Internal Transcribed Spacers (ITS-1) region of DNA obtained from Contracaecum species of Lates niloticus and Oreochromis niloticus showed different PCR products related to Contracaecum spps.