Two specimens of the pelagic nemertean Protopelagonemertes beebei Coe, 1936 were collected in Sagami Bay, Japan. Kimura-2-parameter distance based on the partial sequences (616 base pairs) of cytochrome c oxidase gene between the present material and that previously reported as an unidentified specimen of the genus Protopelagonemertes collected from off California, USA was 5.6%, implying that these are closely related, and may belong to the same species. A description of the internal morphology based on serial transverse sections of the body is provided. The material showed an intermediate character state in the number of proboscis nerves between what had formerly been reported as P. beebei and P. hubrechti (Brinkmann, 1917), posing a question on the species delimitation.
