Identification of tracemakers is of primary importance for evaluating the biotic interactions inferred from bore holes in fossil shell assemblages. Domicile bore holes in the subapical whorls of gastropods produced by spionid polychaete Dipolydora sp., supposed to be commensal with hermit crabs, are common in dead gastropod assemblages from deepwater habitats in the Philippines. These holes exhibit unique features and support a new criterion for the interpretation of nonpredatory borings in fossil gastropods. Diagnostic of these bore holes are: small circular to elliptical outer opening, the presence of weak dissolution of the columella beneath the bore hole, and the presence of a hollowed tube composed of detritus held together with mucus within some gastropod whorls anterior to the hole. The two selection factors of subapical whorls and elongate shells are supplementary criteria for recognition of these holes. Bore holes are recognized here in a deepwater gastropod assemblage from the upper Pliocene Shinzato Formation of Okinawa, Japan, and named Polydorichnus subapicalis n. igen. and isp. These holes are identical to modern examples exhibiting similar site and species selectivity. P. subapicalis has its oldest fossil record in the upper Miocene of the Philippines, was common in offshore assemblages from the Miocene onward, and is a good indicator of occupation by a hermit crab and for commensalism between polychaetes and hermit crabs.