We investigated morphological differences in specimens of the arcid bivalve Scapharca kagoshimensis collected from two sites differing in turbidity in the inner part of Ariake Bay. First, we confirmed if the specimens collected from the two sites were the same species by comparing the sequences of their nuclear 18S ribosomal DNA (18S rDNA) and cytchrome c oxidase subunit I gene (COI) of mitochondrial DNA (mtDNA), since the closely related species S. inequivalvis could be distributed in one site. The results of DNA analyses showed that specimens from both sites belonged to the same species. Shell morphology, gill and posterior adductor muscle size did not differ between the two populations. However, the size of the labial palp was significantly larger in bivalves living in an area of high turbidity compared with those living in an area with low turbidity. This difference could not simply be attributed to differences in meat content because the total weight of the soft body parts did not differ between the two populations. The labial palp is an organ functioning in preingestive particle selection. Hence, the large palps would presumably be a response to high turbidity conditions in which the need for particle processes increases. To the best of our knowledge, this is the first study demonstrating palp size flexibility in arcid bivalves, and such flexibility could be a factor enabling S. kagoshimensis to successfully exploit a wide area of shallow water in the inner part of Ariake Bay.