DNA preserved in sediments was used to study the succession of historic phytoplanktonic communities in a deep lake (Bourget France). DNA was extracted successfully from a sediment core recording the last 100 years. The diatom and cyanobacterial communities were targeted. Cloning-sequencing (18S rRNA, 16S, ITS and 23S rRNA genes) was used to compare distinct regions of the core, corresponding a priori to different trophic periods in the lake (oligotrophic to eutrophic). Clear changes in the diatom and cyanobacterial communities were identified between the analysed time points. Moreover we reconstructed the quantitative distribution of Planktothrix spp. (cyanobacteria) by real-time quantitative PCR (on PC, 16S and mcyA genes). We showed that deep calcareous lakes are favorable environments for an efficient preservation of DNA (high quality sequences obtained) and we revealed that designed qPCR assay could be applied successfully to these laminated sediments. The reconstruction of temporal variations in past community assemblages and biodiversity, using biomarkers, is a promising approach. We identified further areas for future studies in order to optimize the use of DNA biomarkers in lacustrine sediments analysis.