We evaluated the community characteristics and distribution of zooplankton from June 2010 to January 2011 in Bosten Lake. We identified 83 species of zooplankton, including 27 species of protozoa, 42 species of rotifer, 10 species of cladocera, and 4 species of copepoda. The zooplankton assemblage consisted primarily of hackneyed eurythermal species with a few cryophil species. Micro-zooplankton were the most abundant type (>64.8%), whereas macro-zooplankton (chiefly cladocera) dominated the total biomass (>85.2%). The species richness index was highest in summer (1.52) and lowest in winter (0.74). The species diversity index and species evenness index peaked in autumn (3.01 and 0.95, respectively) and were lowest in winter (0.75 and 0.63, respectively). Multi-variate analysis revealed that there were comparatively large differences in zooplankton community structure between the northwest and southwest regions of Bosten Lake. These differences increased between June and October but were lowest in January.