Year-round changes in species composition and flux of calcareous dinoflagellates at station JT (34°09.8′N, 141°59.3′E; water depth, 8942m; trap depth, 916m) are reported. A time-series of thirteen sediment-trap samples of 29 days each, between March 5, 1991 and March 2, 1992, provided materials for this study. Vegetative cysts of a calcareous dinoflagellate, Thoracosphaera heimii, were found to be overwhelmingly dominant forming >95% of the calcareous dinoflagellate associations in all trap samples. Its’ flux ranges from 910,000 shells·m−2·day−1 in May, 1991, to 76,000 shells·m−2·day−1 in September, 1991. Cysts of other calcareous dinoflagellates (Leonella granifera, Calciodinellum albatrosianum and Calciodinellum levantinum) were also found, with a maximum flux of 11,000 shells·m−2·day−1 for C. albatrosianum between December, 1991 and January, 1992. Based on physiological information, we suggest that species flux depends on water mass distribution linked to migration of the path of the subtropical Kuroshio Current. High to moderate flux of T. heimii occurred when the current took a meandering or a straight nearshore pathway. Waters southeast of the current prevailed over the trap station during this time. The most favorable environment, May, 1991, for T. heimii production seems to occur around a shallow thermocline formed above Subtropical Mode Water (STMW) in the waters southeast of the current. The species flux dropped when the current took an offshore pathway and flowed over the trap station. Surface and subsurface waters of the Kuroshio Current, especially during summer to autumn, is not productive of this species. The species flux also dropped while a “cold water mass” (i.e. lower salinity water cut off from the subarctic Oyashio Current) emerged over the trap station. Three cysts, L. granifera, C. albatrosianum and C. levantinum, show broadly similar abundance fluctuations to T. heimii. This close relationship between temporal changes in T. heimii productivity and path migrations of the Kuroshio Current, which is linked to the wind stress field over the North Pacific, should potentially provide information for paleoclimatic reconstructions.