Ciliates are unicellular heterotrophic organisms that play a key role in the planktonic and benthic food webs of lakes, and represent a great potential as bioindicator. In this study, we used the top-bottom paleolimnological approach to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient using metabarcoding techniques applied on sedimentary DNA (sed-DNA). Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes which are more strongly expose to local human pressure. Analyses of the functional groups indicate important restructuration of the trophic food web and changes that are consistent with several well documented environmental changes such as the widespread increase in deep water anoxia, changes in thermal stability and nutrient cycling. Our study demonstrates the potential offered by sed-DNA to uncover information about past ciliate communities on a wide variety of lakes and the potential of using ciliates as valuable indicators, integrating information from the pelagic to the benthic profundal (and littoral) zones. Through trait-based functional community approach, the ciliates provide additional valuable information on ecosystem functioning, thus offering more a holistic view on the long-term changes of aquatic ecosystems.