The genus Henneguya is the second largest within the class Myxosporea, which infects marine and freshwater fish. One hundred Clarias gariepinus specimens were collected alive from a branch of the Nile River in Kafrelsheikh, Egypt. Microscopic and molecular procedures were used to describe how Henneguya fusiformis infects the ovaries of C. gariepinus. The infected fish showed no pathogenic changes except for macroscopic creamy whitish nodules in their ovaries with the highest prevalence during the spring season. The mature spores are spindle-shaped. The total spore length, spore body length and width are 53.4 ± 0.8 (52.5-54.3) µm, 29.8 ± 0.5 (29.2-30.4) µm and 6.5 ± 0.3 (6.1-6.9) µm, respectively. The spore anterior end consisted of two equal polar capsules, located in a tandem position, each one measuring 4.2 × 2.1 µm. The polar filament formed a coil with 6-8 turns. The measurement of the spore end with two extended processes was 24.3 ± 0.4 (23.9-24.8) µm. Phylogenetic analyses of the 18S ribosomal RNA gene sequence revealed that H. fusiformis are clustered together with other myxobolids that are histozoic in channel catfish, Ictalurus punctatus, and Asian Redtail catfish, Hemibagrus nemurus" (Clariidae) in the United States and Malaysia, respectively. To the best of our knowledge, this is the first record of H. fusiformis in Egypt. Additionally, our study is the first record of H. fusiformis in the ovaries of C. gariepinus.