A total of 92 species or taxa of polycystine radiolarians were identified in depth-stratified plankton samples collected from the Tsushima Strait between Japan and Korea in autumn 2006. This assemblage can be divided into three groups: shallow eastern channel, shallow western channel, and bottom western channel. The distribution patterns are most likely related to different water masses. The western channel is influenced mainly by the Taiwan Current and coastal waters, which are characterized by low salinity and high nutrients, whereas water in the eastern channel is mainly from the Kuroshio Current. Cycladophora davisiana, which lives deeper than 500 m in the Japan Sea, was abundant in the western channel at 100–140 m. This suggests that the deeper microzooplankton in the Tsushima Strait are associated with colder and less saline water originating from the greater depths of the Japan Sea.