Abstract: Aphanizomenon sp. is one of the most common bloom-forming cyanobacteria in Chinese freshwater bodies. The bloom, formed by Aphanizomenon, has resulted in serious environmental and ecological safe problems. Therefore, owing to its potential effect, directly or indirectly, on animal and human, Aphanizomenon has attracted great attention by researchers and managements. As already illustrated, many bloom-forming cyanobacteria have developed some sound ecological strategies to form water bloom during evolution, while the mechanism in Aphanizomenon remains still unknown. The increase of phosphorus concentration, a limiting factor at freshwater bodies, is always thought to be responsible to the bloom formation. However, there are relatively few data to study how to respond to the increase of phosphorus levels in Aphanizomenon at present. Therefore, in order to explain the responses to phosphorus in Aphanizomenon, the physiological and ecological functions of Aphanizomenon were selected to discuss in the present study. In this study, the physiological parameters, including the specific growth rate, photosynthesis evolution, maximum electron transfer rate (ETRmax) and alkaline phosphatase activities (APA), were investigated when Aphanizomenon flos-aquae, a type strain of Aphanizomenon, was cultured at different phosphorus concentrations (0.00, 0.02, 0.05, 0.50 and 1.00 mg/L). The results showed that significant decreases were found in the specific growth rate (), the maximum photosynthesis rate (Pm), saturation light irradiance, PSⅡphotochemical efficiency (Fv/Fm), and the maximum electron transfer rate (ETRmax), when A. flos-aquae was inoculated into the Pi levels of less than 0.50 mg/L. On the contrary, significant increases were indicated in the respiration (Rd) of Aphanizomenon when cultured at lower Pi concentrations. It suggested that Pi stress was found in A. flos-aquae when grown at less than 0.50 mg/L Pi concentration, and the stress might directly inhibit photosynthesis efficiency, which resulted in the increase of respiration and the decrease of growth. At the same time, A. flos-aquae increased markedly its activity of alkaline phosphatase (APA) in order to response to the stress since alkaline phosphatase could translate organic phosphate into inorganic phosphate. When cultured at higher Pi concentration more than 0.50 mg/L, the physiological parameters did not markedly change, suggesting that A. flos-aquae could keep a normal growth rate only when the Pi levels reached to 0.50 mg/L or higher. In conclusion, the data suggested that A. flos-aquae could regulate its physiological responses, such as photosynthesis and APA activities, and so on, to deal with Pi stress in order to keep its survival and dominance.