Phylogenetic relationships among twenty two metazoan parasites recovered from seven species of clariid fish from Lake Victoria were analysed using partial 18S rDNA sequences. The 18S rDNA gene was amplified by polymerase chain reaction, directly sequenced, aligned and phylogenies inferred using maximum parsimony. Heuristic bootstrap MP searches yielded one most parsimonious tree (CI = 61%, HI = 39%), which showed that clariid parasites are monophyletic at higher taxonomic levels (Cestodea, Nematodea, Digenea and Crustacea). However the position of two trematodes (Allocredium mazoensis and Clinostomum sp.) and a nematode (Contracaecum sp.) were not stable. Despite the present findings, the study utilised single species from each taxa, hence further analysis with additional sequences from a multitude of species is recommended to further resolve the phylogeny of the parasites of the clariids in Lake Victoria and elsewhere.