Monitoring populations in time is a straightforward way to document evolutionary dynamics in response to environmental change, but requires long-term studies and can not be done in retrospect. Many aquatic organisms produce dormant eggs, the resulting layered egg banks providing an archive of past evolutionary change. Here, we apply a paleogenetics and paleogenomics approach to reconstruct evolutionary dynamics from layered egg banks in the waterflea Daphnia. In the cyclical parthenogen D. magna we will identify associations between candidate genes and environmental changes that will subsequently be experimentally validated. This will be achieved with the screening of populations along well-defined environmental gradients with a broad array of molecular markers. The candidate genes will subsequently also be studied on layered egg banks of populations that experienced well-documented historical environmental changes. Paleogenomics enables extending the time axis for reconstructing evolutionary dynamics to several hundreds of years, offering the potential to go back to the pre-Industrial Revolution era. We will also apply paleogenetics to study evolutionary changes in populations of obligately parthenogenetic D. pulex inhabiting arctic ponds that were exposed to well-defined environmental changes during the past 200 years. This study will provide insights on responses of obligately parthenogenetic populations to environmental change.