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With ease of collection, short life cycles, lack of complex developmental stages, and rapid response to environmental changes, protozoa attract the increasing attention as suitable indicators for bioassessment. In order to reveal the annual variation of protozoan communities and its relation to the environmental conditions in a sub-tropic urban wetland, the protozoan species composition, abundance, diversity, and their correlations with abiotic factors were studied in Xixi wetland, Hangzhou, China. A total of 89 protozoan species comprising 34 ciliates, 13 flagellates, and 42 rhizopods were recorded; 7 of those were the dominant species. The protozoan abundance ranged from 3×104 ind. l-1 to 19.65×104 ind. l-1; ciliates (69.3%) were the primary contributors in terms of relative abundance. The cluster analysis discriminated the protozoan communities into three annual stages: spring, summer-autumn and winter at a 30% similarity level with significant difference. Multivariate correlation analysis showed that temporal variation in protozoan communities was significantly related to the changes of environmental variables, especially water temperature, dissolved oxygen, chemical oxygen demand (COD) and nutrients. Three diversity indices (species richness, diversity and evenness) were significantly correlated with the COD and nutrients. The results demonstrated that the annual variation in protozoan abundance represented a clear seasonal shift in response to environmental changes and thus may be used as a potential indicator for assessing water quality in a sub-tropic urban wetland ecosystem.