<p>Increasing human activity and environmental changes have a complex impact on the evolutionary histories of most biomes. How environmental changes affect genetic evolution of wild populations has become a frequent research theme of biological ecology. Molecular techniques, in conjunction with palaeogenetics, facilitate understanding of the relationship between the genetic structure of wild populations and environmental change. In this study, genes encoding <i>16S</i> rRNA, cytochrome c oxidase subunit 1 (<i>CO</i>I), internal transcribed spacer (<i>ITS</i>), and Na⁺/K⁺ ATPase were used as molecular markers to reconstruct changes in the temporal population genetic structure of <i>Daphnia sinensis</i> based on the analysis of resting eggs from the sediment layers in Lake Chaohu. The genetic variation of the <i>16S</i> rRNA, <i>CO</i>I, <i>ITS,</i> and Na⁺/K⁺ ATPase genes of <i>D. sinensis</i> comprised 0–0.7%, 0–2.5%, 0–9.7%, and 0–15.4%, respectively, and was significantly affected by the total nitrogen and total phosphorus contents. The evolutionary molecular clock analysis predicted that sequences in different layers diverged over the time of 1.3–1.6 million years, which greatly exceeded the real age of the sediment (60&#xa0;years). Phylogenetic analysis showed that genetic variation of the <i>16S</i> rRNA gene occurred the earliest, and the <i>ITS</i> gene had the highest genetic variation. Up to 32% of the Na⁺/K⁺ ATPase gene variation was explained by differences in the total phosphorus content. Moreover, we found evidence that high phosphorus levels may have triggered the directional selection of the Na⁺/K⁺ ATPase gene loci. Our results help to understand better the microevolution of cladoceran populations in eutrophic lakes.</p> Graphic abstract <p></p>