Current surface production in the Banda Sea is primarily controlled by monsoonal forcing, the strength of the Indonesian throughflow and surface salinity, and is sensitive to global climate changes. Therefore, variations of paleoproductivity represented by the abundance of diatoms are estimated to assist in understanding possible hydrological changes during glacial–interglacial cycles since Marine Isotopic Stage 11 (MIS 11). During the interglacials, the enhanced austral winter monsoon (southeast monsoon) encourages deepening of the mixed layer and uplifting of the thermocline, thereby increasing surface production. However, accompanied enhancement of the Indonesian throughflow (ITF) within the interglacials brings warm and less-saline water from the central part of the warm pool water entering the Banda Sea to mitigate development of the upwelling system. Conversely, cooling of the Northern Hemisphere forces the strengthening of the austral summer monsoon (northwest monsoon) to depress the upwelling and reduce production during glacial intervals, whereas the weakening flow of the ITF reduces the influence of low-salinity capping effects and benefits production. Higher abundance of Chaetoceros sp., dominant in upwelling environments, observed in glacials suggests that strength of the ITF is the most important factor in controlling the vertical thermostructure of the Banda Sea. Copyright © 2012 John Wiley & Sons, Ltd.