We describe Phoronis emigi sp. n. as the eighth member of the genus based on specimens collected from a sandy bottom at 33.2 m depth in Tomioka Bay, Amakusa, Japan. The new species is morphologically similar to P. psammophila Cori, 1889, but can be distinguished from the latter by the number of longitudinal muscle bundles in the body wall (56–72 vs. 25–50 in P. psammophila) and the position of the nephridiopores (situated level with the anus vs. lower than the anus in P. psammophila). Using sequences of the nuclear 18S and 28S rRNA genes and the mitochondrial cytochrome c oxidase subunit I (COI) gene, we inferred the relationship of P. emigi to other phoronids by the maximum likelihood method and Bayesian analysis. The analyses showed that P. emigi is closely related to P. hippocrepia Wright, 1856 and P. psammophila Cori, 1889. We describe the morphology of the topotypes and additional material for P. ijimai Oka, 1897. Neither our morphological observations of P. ijimai, nor the phylogenetic analyses based on 18S and COI sequences, contradicts that P. vancouverensis Pixell, 1912 is conspecific with P. ijimai, a synonymy that has long been disputed.