Sea surface temperature and oxygen isotopic records from two well-dated Indian Ocean cores covering the last deglaciation show the occurrence of two periods of increased salinity along the route of warm surface water transport from the Indian to the Atlantic Ocean, one between 18 and 14.5 ka and the other during the Younger Dryas. Our results imply that during these periods, salt accumulated in the tropical Atlantic, creating favorable conditions for an abrupt resumption of the thermohaline circulation and abrupt northern hemisphere warming. Furthermore, we suggest that the observed pattern of millennial climate variability during the last glacial and deglaciation resulted from the interaction between the relatively slow rhythm of expansion and decay of the northern hemisphere ice sheets, and El Nino-Southern Oscillation variability, through changes in the position of the Intertropical Convergence Zone. This interaction generated an oscillator with millennial time response that operated at times of sufficient northern hemisphere ice sheets extent.