Microcystins are hepatotoxic heptapeptides and general tumor promoters produced by several species of the genera Microcystis, Anabaena, Oscillatoria and Nostoc. They are non-ribosomally synthesized via a mixed polyketide synthase/non-ribosomal peptide synthetase system called microcystin synthetase. We have carried out the detection, isolation and structural determination of non-toxic peptides produced together with microcystins by toxic cyanobacteria, which are classified into several groups on the basis of their structures and some of these non-toxic peptides are also non-ribosomally synthesized as well as microcystins. In the present study, we tried to correlate the secondary metabolic peptides produced by the hepatotoxic cyanobacteria with the corresponding peptide synthetase genes. An analytical method using LC-electroscopy ionization MS and photodiode array detection was developed for the exhaustive screening of cyanobacterial peptides in Japanese strains and it was successfully applied to the peptide fractions extracted from these strains. The established method was advantageous over conventional ones using the usual HPLC and matrix-assisted laser desorption ionization time-of-flight MS, because more structural information could be obtained and it is easier to distinguish microcystins from other peptides using this method. Small amounts of other peptides could also be detected by this method. The established method will contribute to the investigation of the relationship between genes encoding the peptide synthetase and secondary metabolic peptides.