These datasets contain plant taxa detected by sedimentary DNA analyses in five lakes in the North-western Alps. The records cover the last 4000/6000 years. The datasets are presented in number of DNA sequences by replicate of analyses (multiple sample, extractions or polymerase chain reactions were performed for each analyzed sediment layer). These datasets were produced to reconstruct past changes in plant composition. They were obtained by applying the DNA metabarcoding approach (Taberlet et al. 2007) on sediment cores retrieved by using the following coring systems: uwitec gravity corer and NIEDERREITER piston corer.