The morphology of two Pseudopolydora species, P. cf. reticulata Radashevsky and Hsieh, 2000 and P. achaeta Radashevsky and Hsieh, 2000 are reported from Japan for the first time. Pseudopolydora cf. reticulata was collected from Japanese tidal flats, and individuals possess the characteristic netlike pigmentation on the dorsum of anterior chaetigers and the longitudinal black band along midline of caruncle. Pseudopolydora achaeta was collected from subtidal bottom mud of Onagawa Bay, and individuals have distinctive characteristics, such as intensive black pigmentation on dorsal and ventral sides of the anterior body and nearly straight vertical rows of major spines on the fifth chaetiger. The morphology of P. cf. reticulata is very similar to that of P. cf. kempi, with which it had been confused in Japan. We analyzed the 18S and 28S rRNA gene sequences of all five Pseudopolydora species recorded from Japan and found strong evidence that they are genetically distinct. Our analysis also suggests that boring polydorids have evolved among non-boring ones; the genus Pseudopolydora, which mostly shows the non-boring form, appears to have remained in a more ancestral condition.