Abstract: Cuspidothrix issatschenkoi formerly Aphanizomenon issatschenkoi, is the potentially toxic cyanobacterium. Nowadays, this species has been discovered on all continents except the Antarctica. The cyanobacterial blooms and toxins caused by C. issatschenkoi from different countries have caused many aquatic environmental problems, however, there are few studies researched on its geographical distribution and ecological characteristics in China. The present study initiated based on the field survey data derived from 87 shallow lakes in the middle and lower reaches of the Yangtze River from June to August 2013, we found C. issatschenkoi occurred in more than half of the freshwater lakes in the investigated area, and its biomass fluctuating from 0.001 to 3.019 mg/L. The correlation analysis between C. issatschenkoi and environmental factors showed that the biomass of C. issatschenkoi is negative with the total phosphorus in freshwater ecosystem, indicated that C. issatschenkoi had better adaptability and competitiveness under the condition of low phosphorus. And there is a positive correlation between its biomass and total nitrogen, thus sufficient nitrogen source in the water may increase the potential risk of forming water blooms by C. issatschenkoi. Since C. issatschenkoi has been reported to be the main cyanobacterial species to synthesis anatoxins in Chinese freshwater bodies, indicating that severe threat in freshwater security may posed by this species. Our results revealed the geographical and ecological characteristics of C. issatschenkoi, which can provide data foundation for the ecological research and management of harmful algae in the future.