Many phototrophic flagellates ingest prokaryotes. This mixotrophic trait becomes a critical aspect of the microbial loop in planktonic food webs because of the typical high abundance of these flagellates. Our knowledge of their selective feeding upon different groups of prokaryotes, particularly under field conditions, is still quite limited. In this study, we investigated the feeding behavior of three species (Rhodomonas sp., Cryptomonas ovata, and Dinobryon cylindricum) via their food vacuole content in field populations of a high mountain lake. We used the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) protocol with probes specific for the domain Archaea and three groups of Eubacteria: Betaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria of Bacteroidetes. Our results provide field evidence that contrasting selective feeding exists between coexisting mixotrophic flagellates under the same environmental conditions and that some prokaryotic groups may be preferentially impacted by phagotrophic pressure in aquatic microbial food webs. In our study, Archaea were the preferred prey, chiefly in the case of Rhodomonas sp., which rarely fed on any other prokaryotic group. In general, prey selection did not relate to prey size among the grazed groups. However, Actinobacteria, which were clearly avoided, mostly showed a size of Ͻ0.5 m, markedly smaller than cells from the other groups.IMPORTANCE That mixotrophic flagellates are not randomly feeding in the main prokaryotic groups under field conditions is a pioneer finding in species-specific behavior that paves the way for future studies according to this new paradigm. The particular case that Archaea were preferentially affected in the situation studied shows that phagotrophic pressure cannot be disregarded when considering the distribution of this group in freshwater oligotrophic systems.KEYWORDS Archaea, mixotrophic protist, selective feeding M ixotrophic behavior, the combination of phototrophic and phagotrophic nutritional modes within a single cell, has been increasingly documented in aquatic systems (1, 2). Phagotrophy occurs in a variety of phytoplankton flagellate groups, including Chrysophyceae, dinoflagellates, prymnesiophytes, and cryptophytes, which comprise some picoeukaryotes (3-5). Currently, there is no doubt of the ubiquity of mixotrophy and its significance in the functioning of planktonic systems. Under oligotrophic conditions, phototrophic flagellates can account for up to 80% of total bacterial grazing (4,6,7).Predation by protists is among the primary mortality factors of prokaryotes in planktonic communities and thus is an important selective pressure. It becomes a structuring factor of the abundance, morphology, composition, and activity of bacterial assemblages (8, 9). The impact of protist predation appears to be modulated by the characteristics of the system (e.g., productivity) and predator and prey traits (10). Over