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Large uncertainties still exist about the long-term mechanisms influencing the hydroclimate variability of southeast Africa where proxy data and model simulations indicate rainfall dipoles between subtropical and tropical areas. The topography of Madagascar, located off the southeastern coast of Africa, modulates these dipoles while its climate is influenced by the position of the Intertropical Convergence Zone (ITCZ) and the Subtropical High as well as the sea surface temperature (SST) of SW Indian Ocean. The island can thus be considered a key location for the understanding of the tropical SE African climatic variability and the interplay between atmospheric patterns. However, the scarcity of continuous records from Madagascar has made the evolution of regional late Quaternary climate and its driving mechanisms difficult to assess. Here, we present a 26-kyr record of the deuterium/hydrogen isotope ratio (δD) of biomarkers (n-alkanes) from the central eastern part of the island at Antananarivo at around 1250 m a.s.l. Preliminary summary pollen data are also presented as a comparison. The δD profiles of aquatic plant and terrestrial plant-derived n-alkanes generally exhibit similar trends implying that they all record changes in the isotope composition of source water, namely meteoric water that recharges soil and lake waters. In this tropical region, the δD variability of precipitation is mainly influenced by the amount effect reflecting the intensity of precipitation associated with the monsoon. We observe: (i) stable and wet conditions during the Last Glacial Maximum, (ii) drier conditions from 18.5 to 15 ka (ka before present) during the Heinrich Stadial 1 (iii) high humidity after 15 ka culminating at the Younger Dryas (YD), (iv) drier conditions from 11.7 ka to 8.2 ka, (v) a return to humid climate until 2.8 ka, and (vi) an arid phase followed by increased wetness after 0.9 ka, although the record is likely influenced by human-induced vegetation changes the last 1.2 ka. This climate signal is similar to other records from the Mozambique Channel but opposite to records from the East African mainland and the subtropical southern Africa, especially between 20 and 25°S. Although there is a good correspondence of our record with insolation- driven migrations of ITCZ during the LGM and the early Holocene, the dipoles are largely consistent with the modern rainfall anomaly and are best explained by the interlinked effects of the SST changes and the variability of the Mozambique Channel Trough.