Deep-sea benthic foraminifera, planktic foraminifer Globigerina bulloides and pteropods have been quantitatively analysed in 451 samples from Ocean Drilling Program (ODP) Hole 716A, to understand both surface and deep-sea palaeoceanographic changes in the equatorial Indian Ocean basin during the late Quaternary (∼444–151 Kyrs). Benthic foraminifera were analysed from > 125 𝜇m size fraction whereas Globigerina bulloides and pteropods were analysed from > 150 𝜇m size fraction. Factor analysis of most dominant benthic foraminiferal species over the studied time span made it possible to identify three biofacies characterizing distinct deep-sea environmental settings at Hole 716A. The environmental interpretation of each species is based on the ecology of recent deep-sea benthic foraminifera. The faunal record indicates fluctuating deep-sea conditions including changes in surface productivity, organic food supply and deep-sea oxygenation linked to changing wind intensities. These changes are pronounced on glacial-interglacial time scales driven by summer monsoon winds.