Cephalocarida is a rare and poorly known class of small benthic crustaceans, consisting of only eleven species belonging to five genera. Thus far, only one species (Hutchinsoniella macracantha) has been studied at molecular level. We report the partial sequences of two phylogenetically important mitochondrial genes (Cytochrome c Oxidase I and Cytochrome b) from the newly discovered Mediterranean species, Lightiella magdalenina. The genetic relationships between the two cephalocarid species are discussed.