A matrix of 24 morphodevelopmental characters and an alignment of small subunit (SSU) and large subunit (LSU) rDNA nuclear and cox1 mitochondrial gene sequences (∼4500 sites) were compiled from up to 12 phoronids including most named taxa, but probably constituting only a portion of worldwide diversity. Morphological data were analysed by weighted parsimony; sequence data by maximum and Bayesian likelihood, both with Phoronis ovalis as the local outgroup. Morphological and sequence-based phylogenies were similar, but not fully congruent. Phoronid rDNAs were almost free from mutational saturation, but cox1 showed strong saturation unless distant outgroups and P. ovalis were omitted, suggesting that many phoronid divergences are old (≥100 Myr). rDNA divergence between named phoronid taxa is generally substantial, but Phoronopsis harmeri (from Vladivostock) and Phoronopsis viridis (from California) are genetically close enough to be conspecific. In another alignment, of 24 taxa, phoronid rDNAs were combined with data from brachiopods and distant (molluscan) outgroups. The relative ages of divergence between phoronids and their brachiopod sister-groups, of the split between the P. ovalis and non-ovalis lineages, and of other phoronid splits, were estimated from this alignment with a Bayesian lognormal uncorrelated molecular clock model. Although confidence limits (95% highest probability density) are wide, the results are compatible with an Early Cambrian split between phoronids and brachiopods and with the Upper Devonian latest age suggested for the P. ovalis/non-ovalis split by the putative phoronid ichnofossil, Talpina. Most other ingroup splits appear to be ∼50–200 Myr old. Inclusion of phoronids with brachiopods in the crown clade pan-Brachiopoda suggests that a distinctive metamorphosis and absence of mineralization are ancestral phoronid apomorphies. Worldwide diversity and possible associations between character-states and life-history attributes deserve comprehensive further study.