Freshwater lakes are important sources of methane (CH4) emissions, by organic matter degradation under anaerobic conditions (methanogenesis). Previous studies suggest that lakes contribute up to 16 % of natural emissions. About 60 % of the CH4 produced is used as an energy source by methaneoxidizing bacteria (MOB--methanotrophs), which could support higher trophic levels, especially Chironomidae (Diptera). Because biogenic methane has a very low stable carbon isotope value, evidence of methane-derived organic-matter assimilation can be tracked by stable carbon isotope analysis in consumers such as chironomids. In some cases, however, chironomid d13C values are not low enough to unambiguously demonstrate methanotroph assimilation and an alternative line of evidence is required. Analysis of ancient DNA (aDNA) from the methanotroph community preserved in lake sediment provides reliable information about past methane oxidation in freshwater lakes. A combination of these two approaches was used to study a sediment core from the deepest zone of Lake Narlay (Jura, France), which covers the last 1,500 years of sediment accumulation. Results show a significant change ca.AD1600, with an increase in the proportion of MOB in the total bacteria community, and a decrease in chironomid headcapsule d13C. These trends suggest assimilation of MOB by chironomid larvae, and account for up to 36 %of the chironomid biomass. The data also provide information about the feeding behavior of chironomids, with evidence for preferential assimilation of methanotroph type I and the NC10 phylum. The combination of aDNA analysis and carbon stable isotopes strengthens the reliability of inferences about carbon sources incorporated into chironomid biomass