Knowledge on ciliate communities in mountain lakes is scarce, even from a morphological perspective, but especially at the molecular and the ecological level. Despite their fundamental role in the aquatic food web by transferring energy to higher trophic levels, most studies still ignore ciliates or only include certain in-depth data. The alpine region is strongly altered by the effects of climate change. For example, glacial retreats can lead to many newly-formed lakes. During the process of glacial retreat, certain particle-rich turbid lakes can lose their connectivity to melting glaciers. This process can turn these lakes into clear habitats which are highly transparent to ultraviolet radiation (UVR). Both stressors, i.e., a high load of glacially derived particles on the one hand, and exposure to incident UVR on the other, can strongly affect the life of water organisms. The main goal of my PhD study was to investigate in detail the ciliate communities of several mainly alpine lakes in respect to their diversity, ecology and response to the incident UVR. Seven study sites were included, i.e., five Austrian lakes situated between 900 and 2,400 m a.s.l. and two Himalayan lakes in Nepal (5,100-5,400 m a.s.l.). This thesis comprises morphogenetic, ecological and experimental approaches to assess: (1) the ciliate plankton community of a mountain lake by microscopy and next generation sequencing (the hypervariable eukaryotic V4 region of the SSU rRNA gene) in order to find out whether amplicon data coincide with the ciliate morphotype inventory, (2) molecular similarities/dissimilarities of the protistan plankton community among different lake types (clear vs. turbid) and biogeographic regions (European Alps and Himalayan mountains), (3) the abundance and diversity of the ciliate communities in two alpine lakes of contrasting transparency by taxonomical work and their interaction with abiotic (physicochemical and optical properties) and biotic components such as possible food resources and predators and, (4) the direct impact of UVR exposure on two Paramecium populations from alpine lakes of contrasting transparency by exposing them to simulated UVR and PAR conditions at two temperatures in the laboratory. The morphogenetic survey revealed that pyrosequencing data do not reflect the morphological data. A possible reason could be the deficient taxonomic resolution of the marker gene at the genus and species level. Additionally, it could also be the lack of ciliate sequences in reference databases. Until this discrepancy is clarified, genetic surveys of the protistan plankton community should be approached with caution and interpreted only at the family level. Nevertheless, the molecular and morphological analyses revealed that alpine lakes harbor highly diverse protistan plankton communities represented mainly by the Alveolata, Stramenopiles, Cryptophyta and Chloroplastida. Differences of the protistan plankton communities were identified among the different geographic sites and lake types. These differences can be attributed to biogeographical aspects and prevailing environmental conditions. The morphological study showed that the abundant ciliate groups were the Prostomatida and Haptorida in both lake types (clear and turbid lake) but the number of ciliate species and abundance was higher in the glacier-fed turbid lake. The incident UVR and PAR and the presence of predatory zooplankton were identified as the main drivers for the ciliates distribution pattern. Finally, UVR experiments demonstrated erratic swimming behavior and a high level of DNA damage in two Paramecium populations. However, their survival was not affected. In conclusion, this thesis highlights an unexpected diversity of protists and particularly, ciliates in alpine lakes. Their appearance is obviously coupled with prevailing environmental conditions in such lakes but the evolution of adaptive strategies and specific traits allow them to thrive in such extreme environments.