During a survey of myxosporean parasites infecting freshwater fishes from the River Nile at Giza Governorates, Egypt between March and September 2016, nine out of 30 specimens of the Nile carp Labeo niloticus (Cyprinidae) were found to be naturally infected with Myxobolus naffari (Myxobolidae). Small macroscopic plasmodia appeared embedded in the host gill tissue accompanied with fusion of the gill epithelia, and atrophy was observed at the site of infection. The host reaction was manifested by the encapsulation of the plasmodia with a thick layer of connective tissue. The plasmodia appeared as white, elongated rods between gill filaments with an intensity ranging from three to eight cysts/fish. The average dimensions of plasmodia were 1.2–2.0 (1.8 ± 0.2) mm long × 0.4–0.7 (0.6 ± 0.2) mm wide. The spores were oval, reaching 9.56–11.2 (10.2 ± 0.2) μm long and 6.5–7.7 (7.0 ± 0.4) μm wide with two equal-sized polar capsules regularly arranged at the anterior pole of each spore. They were 4.51–5.5 (5.1 ± 0.4) μm in length and 1.5–2.0 (1.7 ± 0.2) μm in width. Histological, semi-thin sections were taken through parasite plasmodia and transmission electron microscopic examination of ultrathin sections was performed to describe the developmental stages of the recorded parasite within the host fish.