Freshwater fishes were sampled from the River Nile at different localities in Qena Governorate (Qus, Qift, Dandara, El-Trammsa, El-Maana, Dishna and Nag-Hammady). The investigated fishes are Oreochromis niloticus (180) and Tilapia zilli (66). Out of 246 fishes examined, 61 (24.8%) were found to be infected with myxosporean parasites. The infection rate was 25% of O. niloticus and 24.2% of T. zilli. Eight species of Myxobolus spp. were described from gills and one species was found in blood. The collected parasites are M. agolus, M. heterosporus (type 2), M. clarri, M. heterosporus (type 3) and a myxosporean species had been found infecting gill filaments of O. niloticus. Meanwhile, blood of one O. niloticus fish was found harboring Myxobolus sp.I. M. tilapiae, M. niloticus, M. zilli and M. fahmii were found parasitizing gill filaments of T. zilli. M. heterosporus (type 2) had been studied using scanning electron microscope. Comparisons with closely related species are provided.