Genetic diversity of photosynthetic picoeukaryotes has been investigated at two stations located in Meiliang Bay and East Taihu in Lake Taihu, respectively. Genetic libraries of chloroplast 16S rRNA gene have been constructed by using primer set PLA491F/OXY1313R, biased towards chloroplast of marine algae. The results show that most of photosynthetic picoeukaryotic sequences belong to Cryptophyta, and the rest of them are affiliated with Bacillariophyta, Chrysophyta and Haptophyta. The study can help us take knowledge of the community structure and ecological function of phytoplankton in Lake Taihu.