In this study we show that cylindrospermopsin (a cyanotoxin) content of filaments of Aphanizomenon ovalisporum ILC164 depended on growth on combined nitrogen or nitrogen fixation. Our results also demonstrated that the shift down of cyanobacterial filaments from combined nitrogen to dinitrogen fixing condition resulted in a significant decrease of cylindrospermopsin pool size which resumed a growth rate dependent manner as the heterocyst and nitrogenase formation appeared. The current study indicated that alteration of nitrogen metabolism of Aphanizomenon ovalisporum (Forti) induced changes in cyanotoxin (cylindrospermopsin) metabolism. In addition, this is the first report that isolated heterocysts, the differentiated anaerobic cells for nitrogen fixation of cyanobacteria, did not contain cylindrospermopsin.