Adults of Rhadinorhynchus niloticus, a member of the Rhadinorhynchidae family, were isolated from the intestines of wild Nile perch (Lates niloticus (Linnaeus, 1758); Perciformes: Latidae) caught from the River Nile and its tributaries in Assiut City, Egypt. The parasite was found freely in the intestinal lumen with a prevalence of 10.71%, and the burden varied from one to five parasites per fish. The mean intensity and abundance were 2.16 ± 0.47 (95% CI: 1.33 to 3.17) and 0.23 ± 0.08 (95% CI: 0.11 to 0.43), respectively. The parasite was described using light and scanning electron microscopy. Molecular species identification as well as phylogenetic relationship analysis of the isolated parasite were achieved by sequencing and comparisons of the mitochondrial cytochrome oxidase C subunit I (COI) and nuclear 18S rRNA genes. The sequences were deposited in GenBank under the accession numbers PP859185 and MZ727194. Furthermore, phylogenetic analysis demonstrated that the parasites emerged from a separate branch belonging to the Rhadinorhynchidae family, which was clearly distinguished from other genospecies.