Sea-surface temperature (SST) estimates in the sediment core MD01-2390 based on planktonic foraminiferal species abundances using five different transfer function techniques suggest nearly unchanged or unusually higher temperatures in the tropical southern South China Sea (SCS) during the Last Glacial Maximum (LGM) relative to modern temperatures. These results are in contrast to substantial cooling of 2-5 °C inferred by geochemical (Uk'37, Mg/Ca ratios) and terrestrial proxies from the western tropical Pacific region. Using multivariate statistics we show that the glacial southern SCS harboured unique planktonic foraminiferal assemblages that have no modern analogs. Analyses of faunal variation through the core reveal that planktonic foraminiferal assemblages responded to temperature changes inferred from Mg/Ca data but that this signal is subdued by superimposed variations in the relative abundance of Pulleniatina obliquiloculata and Neogloboquadrina pachyderma (dextral). These species occur in glacial samples at proportions that are not observed in the calibration data set. The glacial high abundance of N. pachyderma (dextral) are interpreted to reflect a seasonal (winter) inflow of cold surface water from the northeast via the Bashi Strait due to the combined effects of an intensified winter monsoon, a southward shift of the polar front and the eastward migration of the Kuroshio Current. In contrast, processes controlling the high relative abundances of P. obliquiloculata during the LGM may be unique to the southern SCS. We propose a scenario involving a stronger (winter) mixing or enhanced upwelling due to an intensified winter monsoon that prevented shallow-dwelling, warm indicators to establish larger populations during the LGM. Our results indicate that a no-analog behaviour of planktonic foraminifera faunas is responsible for the warm glacial conditions in this part of the western Pacific warm pool as implied by foraminiferal transfer functions and that a more significant surface cooling in the region as implied by terrestrial and geochemical (Mg/Ca ratios; alkenone unsaturation index) marine proxies is a more likely scenario.