Photosynthetic picoeukaryotes(PPEs) are major primary producers in lakes, due to their small size, high surface-to-volume ratio and high carbon-specific rate of carbon uptake. However, their diversity is poorly understood in freshwater ecosystems. PPEs community structure of Lake Baiyangdian was investigated in the May 2017, to explore their spatial distribution features and their relationship with environmental factors. The results based on flow cytometric analysis showed that the average abundances of PPEs were 7.59×10⁴ cells/ml, and showed a peak at a certain nutrient level. Regression analysis showed that the abundance of PPEs was affected by total dissoloved phosphorus(TDP) and TN/TP in the lake regions with mesotrophic states, but was related to salinity in the lake regions with eutrophic states. The sequencing results indicated that PPEs were mainly dominated by Chlorophyceae, Bacillariophyceae, Coscinodiscophyceae and Chrysophyceae. At finer level, PPEs community structure was different in the lake regions with two trophic states. Scenedesmaceae, Paraphysomona sp., Haptophyceae and Dinophyceae were prevalent in mesotrophic lake regions, whereas, Haematococcaceae, Chrysophycea sp. and Chromulinale sp. were dominant in eutrophic lake regions. Bioenv analysis results revealed that PPEs community structure was mainly related to those environmental factors, including total dissoloved nitrogen, TDP, TN/TP, nitrate nitrogen and dissoloved oxygen. PPEs structure seemed to be a good ecological indicator for the trophic states of lakes.