Kawaguchipeptin A (1), a novel cyclic undecapeptide, was isolated from cyanobacterium, Microcystis aeruginosa (NIES-88) which produces microcystins. Its structure was determined by two dimensional ¹H-¹H and ¹H-¹³C NMR correlation experiments and confirmed by mass spectral and amino acid analyses. Its absolute stereochemistry was deduced by a combination of spectral and chemical studies.