This is the first report on microcystins from Microcystis aeruginosa Kützing in Taiwan. A total of nine strains of cyanobacteria have been isolated from eutrophic aquaculture ponds and water reservoirs. By mouse toxicity assay, six of the nine strains had LD100 in the range of 25-100 mg per kg mouse for dried bacterial mass. Microcystin-LR and -RR were found in all toxic strains and their contents ranged from 0.11-10.06 microg and 0.08 2.21 microg per mg of dried bacteria, respectively. Microcystin-RA, a minor component found only in M. TN-2 and M. CY-1 strains, was identified as a new microcystin. All three toxins were isolated by a serial separation on an LH-20 column, Si-flash column chromatography and reverse phase HPLC. Toxins were further identified by comparing their FABMS, 1H and 1H-1H COSY NMR spectra with the authentic microcystin-LR. Several other microcystin-like compounds were also found in the cultured strains and their structures are being determined.