Polycystine radiolarian remains were collected during Expedition KS15-4 in a plankton tow sample from 0 to 3000 m water depth at station (Sta.) 1 (30°28.8537′N, 132°24.9532′E). Obtained data from this site provide precious information about radiolarian assemblages living at deep-water depths. Based on R-mode cluster analysis, the surface water is characterized by well known subtropical species such as the Tetrapyle circularis/ fruticosa group and Didymocyrtis tetrathalamus. The subsurface water depths (200–500 m) are characterized by species such as Siphonosphaera abyssi. The intermediate-water depths (500–1000 m) are characterized by relatively high abundances of Larcopyle weddellium and Actinomma boreale, while species such as Cycladophora davisiana inhabit mainly water depths below 2000 m and the Carpocanarium papillosum group inhabits the deep-water depths between 1000 and 2000 m.