Molecular phylogenetic analyses of aligned 18S rDNA gene sequences from articulate and inarticulate brachiopods representing all major extant lineages, an enhanced set of phoronids and several unrelated protostome taxa, confirm previous indications that in such data, brachiopod and phoronids form a well-supported clade that (on previous evidence) is unambiguously affiliated with protostomes rather than deuterostomes. Within the brachiopod-phoronid clade, an association between phoronids and inarticulate brachiopods is moderately well supported, whilst a close relationship between phoronids and craniid inarticulates is weakly indicated. Brachiopod-phoronid monophyly is reconciled with the most recent Linnaean classification of brachiopods by abolition of the phylum Phoronida and rediagnosis of the phylum Brachiopoda to include tubiculous, shell-less forms. Recognition that brachiopods and phoronids are close genealogical allies of protostome phyla such as molluscs and annelids, but are much more distantly related to deuterostome phyla such as echinoderms and chordates, implies either (or both) that the morphology and ontogeny of blastopore, mesoderm and coelom formation have been widely misreported or misinterpreted, or that these characters have been subject to extensive homoplasy. This inference, if true, undermines virtually all morphology-based reconstructions of phylogeny made during the past century or more.