Until now morphological and molecular datasets have failed to agree on phylogenetic relationships within the Crustacea Thecostraca (=Facetotecta, Ascothoracida, and Cirripedia). Three recent phylogenetic studies using 18S ribosomal DNA sequences from selected Cirripedia (Thoracica, Rhizocephala, and Acrothoracica) and Ascothoracida revealed Acrothoracica and Ascothoracida as a monophyletic group. This result disagrees with several larval and spermal morphological features supporting Cirripedia as a monophyletic group. We reanalyzed the same molecular data set including a new Facetotecta sequence using neighbor-joining and maximum likelihood, but incorporating the model of evolution that fits the data best, and maximum parsimony approaches. Our results strongly support the morphological hypothesis that the cirripedes form a monophyletic group, with the Acrothoracica as sister group to the Thoracica Rhizocephala. Moreover, all the phylogenies showed the Facetotecta as the sister group to the remaining Thecostraca (Ascothoracida Cirripedia).