Mitochondrial DNA cytochrome b (cyt b) sequence variation among the clariid fishes of Lake Victoria and the Malagarasi wetland Tanzania were studied between August 2003 and February 2005. Seven species were sampled and together with 26 cyt b sequences from GenBank were used to reconstruct phylogenetic relationships in the family Clariidae. The study revealed two clades: one consisting of the big-head species, Clarias gariepinus and Heterobranchus longifilis, and the other of small-sized species, Clarias werneri, Clarias alluaudi, Clarias liocephalus and Clariallabes petricola. The study further revealed that the genus Clarias is paraphyletic and that H. longifilis clusters deeply inside the Clarias group. Although H. longifilis is thought to be the oldest in evolutionary age in Tanzania, it is not close to the ancestor of the Clariidae family. The results also showed that C. werneri and C. alluaudi are genetically distinct from each other.