Several published records attest to the response of the mid- and low-latitudes to millennial-scale climatic variability. However, forcings, teleconnections and relative leads/lags between the sub-tropics and polar latitudes remain unclear. We focus on the biological response to fluctuations in East Asian Monsoon intensity on sub-millennial timescales in the South China Sea (SCS) and compare these records with those obtained from the NW Arabian Sea dominated by the SW Monsoon. We have analyzed very rapidly accumulating sediments (c. 50 cm/Ka) from the northern SCS recovered during ODP Leg 184 (Site 1144) in a region of high surface productivity c. 400 km SE of Hong Kong. The SCS is the largest semi-enclosed marginal basin of the W. Pacific and is especially sensitive to the influences of the West Pacific Warm Pool and East Asian Monsoon. Nutrient supply from upwelling during the winter monsoon is augmented by cyclonic advection of substantial areas of remotely-forced upwelled water with a high nutrient content both offshore NW Philippines and SW of Taiwan during prevailing NE winds. With temporal resolution <100 yr, our results exhibit millennial-scale variations in both stable isotopes (Nitrogen and Oxygen) and productivity proxies (Chlorins, total N) with evident correlation to the oxygen isotopic record of D-O events from the GISP2 ice-core. Apparently rapid and abrupt increases in productivity record intensification of the winter monsoon during cold periods, whilst remote changes in W. Pacific intermediate source water without the SCS basin appear to control sedimentary isotopic composition. Comparison with similar records in the NW Arabian Sea under the influence of the SW summer monsoon facilitates analysis of the response of the monsoon system to changes in vegetation, albedo and pressure gradient over the Himalayan-Tibetan Plateau (HTP). Monsoon intensity is clearly tightly coupled to high latitude climate change. Variations in seasonal response on the HTP produce quite different responses in areas affected by the two monsoon systems, with important regional feedback effects. Non-concordant variations in winter and summer monsoon intensity respectively offer an intriguing insight into the most likely processes connecting the monsoon system to global records of rapid climate change.