The lophophorates are mainly marine, sessile invertebrates that are characterized by a lophophore, a horseshoe-shaped tentacular filter apparatus surroundingthe mouth opening. Lophophorata comprises three divergent lineages, Phoronida, Brachiopoda and Ectoprocta (Bryozoa). Their phylogenetic relationships to other metazoan phyla as well as to each other have long remained unclear. Based on ontological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem-group of Deuterostomia. In contrast, phylogenomic analyses indicated that the lophophorates are more closely related to trochozoans than to deuterostomes in accordance with previous molecular analyses. The phylogenomic studies supported monophyletic Brachiozoa including Brachiopoda and Phoronida as ell as Polyzoa including Ectoprocta, Entoprocta and Cycliophora, thus rendering Lophophorata polyphyletic. In contrast to previous molecular phylogenetic studies, the phylogenomic analyses presented here indicate that Lophophorata are monophyletic and that phoronids are the sister-group of ectoprocts. The conflicting results might be due to compositional bias resulting in systematic errors in former phylogenetic studies. The monophyly of Lophophorata would imply that the lophophore and the epistome are synapomorphies of the lophophorate lineages. Radial cleavage may be another apomorphy of Lophophorata. However, among phoronids spiral cleavage is known as well, indicating that the cleavage pattern has changed several times within lophophorates.