Here we provide a large dataset on genetic plant diversity retrieved from surface sedimentary DNA (sedDNA) of lakes from Siberia and China spanning over a large environmental gradient. Our dataset encompasses sedDNA sequence data of 244 surface lake sediments and 3 soil samples originating from Siberia and Chinese lakes. We used a PCR-based metabarcoding approach combined with Next-Generation Sequencing to assess the modern and local plant diversity in and around the analysed lake localities. As...