Radiolarian assemblages in 69 surface sediment samples from the Japan Sea were moderately diversified, consisting of about 100 taxa in total, although only a few species accounted for a large proportion of most assemblages. First, the assemblages were often dominated by deep-dwelling species: Cycladophora davisiana, Actinomma leptodermum, A. boreale, A. langii, and adult forms of Larcopyle buetschlii. These species were restricted to great depths and were characteristic of the cold, oxygen-rich deep water that fills deep basins of this marginal sea, the so-called Japan Sea Proper Water. Second, although the observed Japan Sea assemblages included some subtropical elements, such as the Dictyocoryne and Euchitonia groups, Didymocyrtis tetrathalamus and the Tetrapyle octacantha group, many of the major temperate and subarctic elements of the North Pacific were essentially excluded. The semi-enclosed topography of the Japan Sea is most likely responsible for the dominance of certain subtropical surface dwellers as well as for the near-absence of transitional and cool water species from corresponding latitudes of the North Pacific. Q-mode cluster analyses of the relative abundance data of the radiolarian species distinguished three faunal provinces that reflect the modern surface water circulation and the distributions of the upper water masses, including the Tsushima warm current and the Liman cold current. These results suggest that the radiolarian assemblages are strongly related to the present hydrography of the Japan Sea and can therefore be used as environmental proxies in this region.