Lake Poyang is one of the two lakes naturally connecting with Yangtze River, with a dramatic and regular water level fluctuation every year. Data of the weekly monitoring from May to November in 2013 was used to study the variations of Anabaena and its heterocyst and the influence factors. It was showed that Cyanophyta was a subdominant species in Lake Poyang. Cyanophyta biomass was accounted for about 57% of total phytoplankton biomass, and Cyanophyta temporarily became the dominant species replacing diatoms in August. The dominant species of Cyanophyta were nitrogen-fixing Anabaena due to the high water temperature and suitable nutrient in summer and autumn. The nitrogen and phosphorus ratios were around 15 in the study period. Anabaena produced heterocyst and became the dominant species of Cyanophyta, reflecting relatively nitrogen deficiency in Lake Poyang. The results can provide a theoretical basis for the protection and utilization of Lake Poyang.