Abstract: Aphanizomenon has been widely reported in many freshwater bodies, and was regarded as one of important bloom-forming cyanobacterial strains. Owing to its effect, directly or indirectly, to animals and human beings, great attention has been focused on the formation mechanism by researchers in areas such as, aquatic ecology, phycology, environmental science, and so on. In China, Aphanizomenon bloom has resulted in many environmental and ecological problems. As already illustrated, bloom-forming cyanobacteria has developed some sound ecological strategies to form water bloom with a series of special physiological mechanisms and adaptation characters during evolution. However, the physiological mechanisms and adaptation characters in Aphanizomenon remain largely unknown. Previous study in our laboratory had shown that three types of Aphanizomenon, A. flos-aquae, A. gracile and A. issatschenkoi, were the most common strains in Chinese freshwater bodies. Due to the limitation of samples and knowledge, however, the physiological characters were not compared in the three-type strains so far. Therefore, in order to further explore their knowledge and investigate the bloom-forming mechanism in Aphanizomenon, in the present study, their morphological and physiological characteristics, including the ratio of length and width in vegetative cell, heterocyst and akinete, growth rate, pigment composition, photosynthetic O2 evolution, and the electron transport rate (ETR), were compared in A. flos-aquae, A. gracile and A. issatschenkoi. The results indicated that some morphological differences were found in the frequency distributions for length/width ratios of vegetative cells, heterocyst, and akinetes. Among them, the most significant difference was found in the akinetes, suggesting that the length/ width ratios of akinetes could be regarded as a taxonomic unit in the genus Aphanizomenon. Moreover, physiological differences were also showed in three types of Aphanizomenon. Compared with the strains of A. flos-aquae and A. issatschenkoi, the strains of A. gracile displayed higher PC contents. However, the strains of A. gracile showed significantly lower chlorophyll α, carotenoid contents, maximum photosynthesis (Pm), apparent photosynthetic efficiency (α), and maximal electron transport rates (ETRmax) in comparison with the other strains of Aphanizomenon. It suggested that the strain of A. gracile showed lower competitive abilities in photosynthesis when compared with the strains of A. flos-aquae and A. issatschenkoi. In addition, similar physiological features, such as the value of Pm and ETRmax, pigment contents and specific growth rate (μ), were found in A. flos-aquae and A. issatschenkoi. These data suggested that the three morphological strains of Aphanizomenon could be divided into two types based on their physiological characterizations, namely, A. gracile-type and A. flos-aquae/issatschenkoi-type, and indicated that the strains of A. issatschenkoi might be potential bloom-formation strains as the same as the strains of A. flos-aquae and must be played a considerate attention due to its toxicity.