Lake Annecy (45° 51' N- 6° 10' E, 446 m a.s.l) is the third largest natural lake in France. It is monomictic and deep (max. depth: 65 m). The lake is often considered as the “cleanest lake in Europe". Lake Annecy was oligotrophic until first signs of eutrophication were noticed in the early 1940's. Water quality degraded until the end of the 1960's. A remediation plan implemented in 1967 resulted in the return to an oligotrophic state. Given the lack of detailed instrumental data before the 1970's, we have developed a paleolimnological approach to assess the trophic history of Lake Annecy during the last 150 years. Chironomid subfossil assemblages and organic matter (Corg, Norg) were studied at high resolution in three cores distributed along a bathymetric transect (30 m, 56 m and 65 m). Chironomid fauna and organic matter analysis of the deepest core suggest a major shift in oxygen conditions at ca. 1930. Oxyphilous taxa were replaced by hypoxia-tolerant taxa. The last decade (i.e. since 2000) is characterized by the near-complete disappearance of the profundal fauna likely linked to the prevalence of anoxic conditions. Parallel analysis of the transect cores can pinpoint the timing and the extent of the hypo/anoxia in the water mass: hypoxic levels reached 56 m at ca. 1940, and 30 m at ca. 1950. During the last 3 decades, no sign of recovery in the chironomid communities could be seen at any depth. This study highlights the degraded state of modern chironomid fauna compared to its pre-1930 state despite the reoligotrophication evidenced from the chemical survey of pelagic water. Our results emphasize the relevance of our paleolimnological approach based on intra-lake coring transects and benthic indicator analysis for the reconstruction of the recent trophic history of lakes and assessment of their present state.