We report on the detection, in a sediment core drilled in Lake Le Bourget (French Alps), of a fossil molecule (miliacin) that was synthesized by broomcorn millet cultivated in the watershed, and then exported to the sediment. The variation in abundance of this molecule allows us reconstructing the history of millet cultivation around Lake Le Bourget. Our results support the introduction of millet around -1700 BC in the region. After an intensive cultivation during the Late Bronze Age, the failure of millet cropping during the Hallstatt period coincides with a phase of climatic deterioration. Millet cultivation recovers during the Roman and Mediaeval periods before falling most probably due to the introduction of more productive cereals. These pioneering results constitute the first continuous record of an agrarian activity for the last 6000 yrs and emphasize the close relationships between local hydrology, land use and agro-pastoral activities around Lake Le Bourget.