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We have been able to reconstruct the changes that have occurred in the phytoplankton community of Lake Baikal over the past 2.8 million years (Ma) by measuring the abundance of residual steryl chlorin esters (SCEs) in the 0–100m section of the 600 m long BDP98 sediment core. The sterol composition of SCEs showed remarkable variations among interglacial periods, and green algae and dinoflagellates, apart from diatoms, had been abundant in Lake Baikal until 1.2 Ma ago.