The phylogenetic position of the brachiopods has been controversial. Many traditional classifications have considered brachiopods (and other lophophorates) to be basal deuterostomes, based on several classically deuderostomic characters: initial cell division of the egg (cleavage) is radial (the cells are arranged in rows, as opposed to spiral cleavage); enterocoelic development leads to a three part body plan; and the mouth is not derived from the blastopore. However, some brachiopods and other lophophorates show exceptions to these characters and other analyses have allied the lophophorates with the protostomes. Molecular phylogenetic work with many independent genes provides consistently strong support for the formal reclassification of the brachiopods as the sister group to pheronids in a group called the “Lophotrochozoa,” essentially derived protostomes (along with molluscs and annelids), and interprets the classical deuderostome characters as more labile and less informative than previously considered. Molecular reconstructions have not allowed much understanding of the relationships within the Lophotrochozoa, but there is much support for a sister relationship between the brachiopods and the phoronids.

(Halanych et al. 1995)