LC/MS/MS under ion trap conditions was used to analyze microcystins produced by cyanobacteria. Tandem mass spectrometry using MS2 was quite effective since ions arising from cleavage at a peptide bond provide useful sequence information. The fragmentation was confirmed by a shifting technique using structurally-related microcystins and the resulting fragmentation pattern was different from those determined by triple stage MS/MS and four sector MS/MS. Analysis of a mixture of microcystins in a bloom sample was successfully performed and two new microcystins were identified by LC/MS/MS under ion trap conditions. Thus, LC/MS/MS under ion trap conditions is effective for the structural characterization of microcystins.