The sequence of 18S rDNA was used to analyze the phylogenetic relationship of three thecostracans, Verruca spengleri, Paralepas palinuri, and Dendrogaster asterinae, with respect to other thecostracan crustaceans whose 18S rDNA sequences were reported previously. The ascothoracidan Dendrogaster is grouped with the other ascothoracidan, Ulophysema. Verruca, a representative of the Verrucomorpha, is located among Ibla, Calantica, and the four balanomorphs analyzed. Our finding that Verruca clusters within the Balanomorpha does not agree with the suggestion that the Verrucomorpha and the Balanomorpha evolved independently and that the order Sessilia is a biphyletic taxon. Paralepas, which belongs to the Heterolepadomorpha (pedunculate cirripeds lacking shell plates) that were regarded as presenting plesiomorphic features of the pedunculates, is placed internally within the Lepadomorpha. This raises the possibility that the Heterolepadomorpha do not represent plesiomorphic features of cirripeds. Accordingly, Paralepas may be regarded as a true lepadomorph in which the loss of shell plates is apomorphic. Our study emphasizes the importance of molecular data in understanding thecostracan evolution.