Microcystins are a group of cyclic peptides which are commonly produced by freshwater cyanobacteria and are harmful to humans and other animals when ingested. As the toxicity of microcystins varies according to their structure, it is important to understand the environmental variables which influence microcystin congener abundance. Because of the differential levels of nitrogen in amino acids incorporated into microcystins, nitrogen concentration might play an important role. During this study, Microcystis CAWBG11 was grown in batch culture until nitrogen-deplete. Over the duration of the study, the relative abundance of the microcystin congeners present shifted. The relative abundance of the arginine-containing microcystins decreased, whilst the congeners which did not contain arginine increased. These changes coincided with a large decrease in nitrate concentration to 0.35 % of initial levels. Linear regression of log10 microcystin content and nitrate concentration revealed slopes which were dependent upon the number of arginine residues present in the toxin. This modulation in microcystin congener relative abundance was likely to be due to scarcity of the nitrogen-rich arginine during periods of nitrogen limitation. During the experimental period the relative abundance of congeners with a single arginine residue at position-2 did not change (p > 0.05), whilst the relative abundance of the congeners with a position-4 arginine decreased significantly (p ≤ 0.001). Our results suggested that there arginine in the microcystin structure may be selectively modulated. Furthermore, the relative toxicity of the nitrogen-depleted culture was found to be reduced (15 % lower) compared with the starting culture.