A Dipolydora species (Polychaeta: Spionidae) was found in mud tubes attached to the larger tubes of the chaetopterid polychaete Chaetopterus cautus in Peter the Great Bay of the Sea of Japan. The worms were close in morphology to D. carunculata, a borer of various calcareous substrata and sponges described earlier from the same area. The chaetopterid-associated tube-building individuals usually differed from shell-boring individuals by the presence of black pigmentation on palps. However, some of them were not pigmented and appeared almost identical to D. carunculata. Isozymes of the tube-building and shell-boring individuals were compared using starch gel electrophoresis. Two of 16 studied isozyme loci proved diagnostic and unequivocally demonstrated the presence of two distinct species. The chaetopterid-associated individuals are described here as a new species, D. melanopalpa. Unbiased Nei's genetic distance between D. melanopalpa and D. carunculata (D=0·949) as well as the level of intraspecific genetic variation in either of them (D. melanopalpa, He=0·206±0·054; D. carunculata, He=0·239±0·044) are high and comparable to those of other electrophoretically studied polydorids. In contrast to other examined polydorids, D. carunculata and D. melanopalpa have the same numbers of expressed isozyme loci.