Drastic environmental conditions such as elevated temperature, abrupt pH variation, low turbulence, and high nutrient inputs can enhance the development of toxic cyanobacterial blooms in lakes and reservoirs. This study describes the occurrence of four microcystin variants (MC) in a bloom in the eutrophic reservoir Billings, in São Paulo City. The bloom sample was collected in October 2003, and Microcystis were the main genus found. The MC were separated and purified by reverse phase high performance liquid chromatography (RP-HPLC). Their structures were elucidated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) and four MC variants were determined: MC-RR, MC-LR, MC-YR, and MC-hRhR. MC-hRhR is described for the first time as a new variant of MC with two homoarginines at positions 2 and 4 in its structure. ESI-MS/MS analysis thus provides a powerful and convenient tool for the determination of variants of MC. These results represent an important contribution to the knowledge of the biochemistry of toxic cyanobacteria and their toxins, specifically in São Paulo State.