The three currently recognized species comprising the pelagic polystiliferous hoplonemertean genus Protopelagonemertes Brinkmann, 1917 are supposedly distinguishable chiefly with respect to the number of proboscis nerves: 29 (varying from 22 to 30) in P. hubrechti (Brinkmann, 1917); 19–21 (varying from 19 to 22) in P. beebei Coe, 1936; and 36 in P. joculatori Van der Spoel, 1988. A single specimen collected off the Pacific coast of Hokkaido, Japan, herein identified as P. beebei, was found to possess 19–23 primary proboscis nerves. In addition to the primary proboscis nerves, the material also possessed 12–16 secondary proboscis nerves, which are discernible from the primary nerves in that they coexist with putative glial cells. Although secondary proboscis nerves have been identified in some other species in the Pelagica, they have not previously been described for any members of the Protopelagonemertes. Our findings thus prompted us to question the validity of morphological species delimitation within this genus, given that the distinction between primary and secondary proboscis nerves has previously not been taken into consideration. Close examination of the specimen in the living state revealed that it is characterized by a pair of cephalic furrows, a structure commonly found in benthic representatives of the phylum, but herein confirmed for the first time among the Pelagica. A 658-bp partial sequence of the mitochondrial cytochrome c oxidase subunit I gene from the newly examined specimen was found to be identical to sequences derived from two other specimens previously collected in Sagami Bay, thereby indicating that P. beebei may occur commonly in Japanese meso- to bathypelagic waters.