A certified reference material (CRM) for microcystins has been prepared by the National Institute for Environmental Studies (NIES). Microcystins are hepatotoxic cyclic peptides produced by cyanobacteria in eutrophic water bodies. At least seven microcystin variants were found by HPLC analysis of the NIES CRM, of which [Dha(7)]microcystin-RR and -LR were the major microcystins present. Because of the lack of available standards we determined the total microcystin concentration in the CRM by the MMPB method, and elucidated the structures of the main individual microcystin variants following their isolation. Analyses of NMR and MS spectra indicated that the remaining minor variants in the CRM were [D-Asp(3), Dha(7)]microcystin-RR and -LR, and [Dha(7)]microcystin-YR, -ThTyrR, and -HilR. The CRM is valuable not only as a standard material for the quantitation of total microcystins but also for the identification of individual [Dha(7)]microcystin variants.