Biostratigraphy of conodonts is widely used for age assignment of Permian strata. In this paper, we report conodonts from the limestone of the Nabeyama Formation deposited on a pelagic seamount in Panthalassa, which is an oceanic realm where Permian conodont data are scarce compared to other oceanic realms. Samples collected from the lower part of the Nabeyama Formation yielded Mesogondolella idahoensis (Youngquist, Hawley and Miller) and Sweetognathus hanzhongensis (Wang), which indicate a late Kungurian age. Previous studies and fusulinids obtained in this study indicate that the studied samples belong to the Parafusulina yabei biozone. Therefore, the Parafusulina yabei Zone includes the uppermost Kungurian. Mesogondolella idahoensis and Sweetognathus hanzhongensis are respectively regarded as cool and warm water species. Hence, the distribution of cool and warm water conodont species may have overlapped in pelagic Panthalassa during the late Kungurian.