Abstract: The structural features of ciliate communities can be used to evaluate environmental quality. The aim of this study was to explore the responses of ciliates to environmental change in alpine wetlands and to try to estimate the environmental quality of the Gahai alpine wetlands based on the structural characteristics of the ciliates communities. Species diversity, characteristics of the ciliates community, seasonal distribution of ciliates, and functional-trophic groups were studied and analyzed using the non-flooded Petri dish method, live observations, and a silver staining method from January 2015 to October 2015. In total, 162 species of ciliates were identified, including 30 unnamed species. These 162 species belonged to 66 genera, 46 families, 13 orders, and 3 classes. In this habitat, Kinetofragminophorea was the dominant class with 78 species, accounting for 48.15% of the total number of ciliate species. The next most dominant glass was Polyhymenophorea with 51 species. The number of ciliate species was significantly associated with the temperature and soil moisture content at each site (P<0.05), and more species were detected in summer and autumn than in spring and winter. Analyses of functional-trophic groups of ciliates showed that Bactivores-detritivores was the main group with 118 species, accounting for 72.84% of the total. Some members of this group consumed both algal and debris and others consumed only algal debris. Algivores were the next most dominant group with 51 species, accounting for 31.48% of the total. The main predators were raptors, and nonselective omnivores also fed on ciliates. The results showed that the diet of ciliates in the Gahai alpine wetland is a typical pyramid-type and the community structure of ciliates is stable.