The phylogenomic approach has largely resolved metazoan phylogeny and improved our knowledge of animal
evolution based on morphology, paleontology, and embryology. Nevertheless, the placement of two major
lophotrochozoan phyla, Entoprocta (Kamptozoa) and Ectoprocta (Bryozoa), remains highly controversial: Originally
considered as a single group named Polyzoa (Bryozoa), they were separated on the basis of morphology. So far,
each new study of lophotrochozoan evolution has still consistently proposed different phylogenetic positions for
these groups. Here, we reinvestigated the placement of Entoprocta and Ectoprocta using highly complete datasets
with rigorous contamination removal. Our results from maximum likelihood, Bayesian, and coalescent analyses
strongly support the topology in which Entoprocta and Bryozoa form a distinct clade, placed as a sister group to
all other lophotrochozoan clades: Annelida, Mollusca, Brachiopoda, Phoronida, and Nemertea. Our study favors
the evolutionary scenario where Entoprocta, Cycliophora, and Bryozoa constitute one of the earliest branches
among Lophotrochozoa and thus supports the Polyzoa hypothesis.