A continuous 740-kyr Quaternary sedimentary sequence containing abundant siliceous microfossils was recovered from Hole C9001C during the D/V Chikyu 2006 Mission off the Shimokita Peninsula, Japan. This region is characterized by mixed water reflecting the influences of one warm current (Tsugaru Current), one cold current (the Oyashio Current), and several intermediate and deep water masses. Polycystine radiolarians (a siliceous microfossil group) are useful for reconstructing paleoceanographic changes in this region during the Quaternary because of their ecological properties in these types of deep-sea sediments. This paper illustrates and reviews the taxonomic features of all the polycystine species encountered during this study. A detailed taxonomy is presented because different taxonomic names have been applied, even to the same morphospecies, in many cases. The taxonomic classification of 104 species belonging to three orders (Collodaria, Spumellaria, and Nassellaria), 16 superfamilies, 33 families, and 66 genera was verified by comparison of the holotypes and the relevant name-bearing specimens in accordance with the International Code of Zoological Nomenclature to the extent possible. The taxonomic classification system was updated with reference to both recent morphological taxonomic schemes and molecular phylogenetic analyses. This paper also provides a detailed synonym list of each previously illustrated species from the northwestern Pacific Ocean in order to standardize applicable taxonomic names for the same morphospecies. In addition, a new family (Amphisphaeridae Suzuki fam. nov.) and a new replacement name (Lithelius haeckelispiralis Matsuzaki and Suzuki, nomen nov. for Lithelius spiralis of Haeckel in 1861 [not Ehrenberg in 1840]) are described, and the diagnoses of the genus Tholomura and the family Lychnocaniidae are emended.