Herein, the morphological and genetic features of the larval specimens of anisakine nematode, isolated from Ylistrum japonicum (Pectinidae) collected from Japanese waters, were examined. Although the specimens were identified as members of the genus Sulcascaris, they were genetically divergent from Sulcascaris sulcata, which is currently the only member of the genus. The present study highlights the possibility that the Sulcascaris population inhabiting Japanese waters represents a unique taxonomic position within the genus Sulcascaris. Additionally, given that many pectinid scallops have been reported as intermediate host of S. sulcata, the present study implies that pectinid scallops may also represent the primary intermediate hosts for the present Japanese Sulcascaris species. Because S. sulcata infections can cause discoloration in the meat of scallops, regular monitoring of the prevalence and intensity of Sulcascaris infections is required to predict the impact of the infections on the market.