Sewage treatment processes can be considered as artificial ecosystems, in which eukaryotes are key microbial components. Protozoans and metazoans are often used as indicators of treatment performance. Eukaryotes are the primary predators of prokaryotes; their predation of dispersed bacteria improves sludge sedimentation and effluent water quality in terms of turbidity, biological oxygen demand (BOD), and suspended solids (27), and also decreases the risk of exposure to bacterial pathogens (28). Some Rotifera lineages specifically graze on filamentous fungi that are known to cause bulking in activated sludge (10), and these organisms can, therefore, be used to prevent sludge bulking. Furthermore, recent studies reported the useful implementation of fungi for granular formation in sewage treatment processes (35) as well as the degradation of cellulose, hemicellulose, and lignin biomass (7). Fungi are known to contribute to denitrification, and some can grow under various O2 conditions (concentrations) through three different energy-yielding metabolic pathways: O2 respiration, denitrification (nitrite respiration), and ammonia fermentation (13). Some eukaryotes belonging to the Rhizaria have been reported to accumulate nitrate under aerobic conditions and to respire using this accumulated nitrate through denitrification under anoxic conditions (31). Due to these important processes, the contribution of eukaryotes to denitrification in ocean sediments is estimated to be equal to that of bacteria (29); thus, eukaryotes may also play a significant role in the removal of carbon and nitrogen in sewage treatment processes. The eukaryotes involved in sewage treatment processes have traditionally been identified morphologically and enumerated by microscopic observations. However, morphological identification is often hampered due to limited or difficult diagnostic criteria for some taxa and the time-consuming processes necessary to acquire identification expertise. Minidiscus cells are easily overlooked because of their small size (1.9–7.5 μm) (25). Furthermore, the functional identification of eukaryotes requires that they are isolated, which can be difficult, especially for small eukaryotes. Thus, the role played by eukaryotic species in many environments—including wastewater treatment processes—remains unclear. These limitations have driven the development of alternative (i.e., molecular) identification methods. The phylogenetic diversity of eukaryotes has been investigated by the construction of 18S rRNA gene clone libraries or tag pyrosequencing methods (3, 25, 33). The molecular diversity of eukaryotes in activated sludge sewage treatment processes has also been investigated (8, 9, 23, 26, 27, 36). These studies investigated specific members of eukaryotes (e.g., Ciliophora and Fungi) or eukaryotes in lab-scale reactors with a small number of clones. Thus, there have been no comprehensive investigations of eukaryotic molecular diversity in full-scale sewage treatment processes, and the diversity and roles of eukaryotes there consequently remain unclear. Eukaryotic communities in sewage treatment processes are influenced by the type of process and operating conditions (6). Various processes are employed to treat sewage, and each full-scale sewage treatment plant receives different amounts and concentrations of sewage, resulting in different operational conditions. Therefore, the eukaryotic compositions of full-scale sewage treatment plants are expected to be highly diverse, and previously unrecognized eukaryotes may be present and play important roles. We here investigated the eukaryotic communities of 9 sludge samples collected from 3 different full-scale sewage treatment processes (activated sludge [AS], anoxic/oxic activated sludge [AO], and oxidation ditch [OD]) by constructing 18S rRNA gene clone libraries. We identified core and shared eukaryotes in sewage treatment processes. Furthermore, the results obtained showed that sewage treatment processes can be characterized by a greater diversity of uncultured eukaryotes than was previously recognized.