The present study was carried out on 360 of two species of freshwater fishes (200 Oreochromis niloticus and 160 Clarias gariepinus, which were collected randomly and seasonally from different localities in Ismailia governorate from December 2017 to November 2018. Naturally infested fishes revealed no phathognomonic clinical signs except dark coloration and ulcers on skin in O. niloticus and Cl. gariepinus. Postmortem examination showed hemorrhages, abrasions in the skin, presence of yellow cysts embedded in musculature and enlargement of liver with yellowish discoloration in both O. niloticus and Cl. gariepinus. The total infestation rate was 70%; in O. niloticus (62%) and in Cl. gariepinus (80%). The isolated monogenetic trematode was Cichlidogyrus tilapiae from gills of O. niloticus. The isolated digenetic trematodes were Orientocradium batrachoides, Astiorema reniferum and Afromacroderoides lazera from the intestine of Cl. gariepinus. Eumesenia aegypticus was isolated from the intestinal lumen of O. niloticus, while encysted metacercariae (EMC) were isolated from different organs of infested O. niloticus. Confirmation of trematode infestation was done by using molecular diagnosis (PCR). Seasonal distribution and histopathological examinations were also recorded and discussed.