Phoronids can be a major component of benthic and planktonic marine communities. Currently, the phoronid world fauna includes ten recognised species, known from adults; however, at least 32 larval forms have been described or documented. This study examined the morphology and 18S rRNA and 28S rRNA genes of two phoronid larvae abundant in Vostok Bay, Sea of Japan. One type was identified as the larval stage of Phoronopsis harmeri, although some distinctive features of this larva differ from the typical description. The morphological and molecular characteristics of the other larva did not match those of described species. According to our morphological results, this second actinotroch larva belongs to the genus Phoronis, but differs morphologically and molecularly from all the known species in the genus, all of which are represented in GenBank for the markers employed here. Taken together, our data suggest that the second actinotroch larva belongs to an undescribed phoronid species. The adult form of this actinotroch has never been identified, but our data suggest a close relationship with Phoronis pallida. The existence of a putative new phoronid species is also confirmed by presence of competent phoronid larvae, which are found in different aquatic areas, have a unique set of morphological features, and whose belonging is still not established.