A new species of spionid polychaete, Polydora onagawaensis, is described from mollusk shells in Pacific waters of northeastern Japan. Its nuclear 18S rRNA gene sequence as well as its morphology, reproductive features, life history and infestation characteristics are reported. Polydora onagawaensis sp. nov. belongs to the Polydora ciliata/websteri group and has a moderate size and variable black pigmentation on the palps and body. Up to 115 worms were found boring in a single scallop shell from suspended cultures in Onagawa Bay, with significantly higher numbers in the right than in the left valve. Females repeatedly deposited a string of egg capsules from around October to June (seawater temperature was below 15°C). The larvae developed inside the egg capsules for 2 wk (10°C, laboratory conditions), until the 3-chaetiger stage, before being released as planktonic larvae. The main spawning occurred in December, recruitment onto the shells increased after January, and most large worms disappeared between July and October. Thus, the estimated life span is around 1.5 yr after settlement. Details on biology and gene information not only contribute to distinguishing the species from other polydorids similar in morphology, but also allow control of polydorid infestation in mollusk aquaculture.