Microcyclamide (1), a cytotoxic cyclic hexapeptide, was isolated from the cultured cyanobacterium Microcystis aeruginosa (NIES-298). Its structure was elucidated to be 1 on the basis of two-dimensional (1)H-(1)H, (1)H-(13)C, and (1)H-(15)N NMR correlation experiments and the HRFABMS measurement. The absolute stereochemistry of the asymmetric centers was determined by the Marfey's method. This peptide showed a moderate cytotoxicity against P388 murine leukemia cells.