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The Australian–Indonesian monsoon is an important component of the climate system in the tropical Indo–Pacific region. However, its past variability, relation with northern and southern high-latitude climate and connection to the other Asian monsoon systems are poorly understood. Here we present high-resolution records of monsoon-controlled austral winter upwelling during the past 22,000 years, based on planktic foraminiferal oxygen isotopes and faunal composition in a sedimentary archive collected offshore southern Java. We show that glacial–interglacial variations in the Australian–Indonesian winter monsoon were in phase with the Indian summer monsoon system, consistent with their modern linkage through cross-equatorial surface winds. Likewise, millennial-scale variability of upwelling shares similar sign and timing with upwelling variability in the Arabian Sea. On the basis of element composition and …