Micropeptins 88-A to 88-F (1-6) have been isolated from the cyanobacterium Microcystis aeruginosa (NIES-88). Their structures were determined by two-dimensional ¹H-¹H and ¹H-¹³C NMR correlation experiments and confirmed by mass spectral and amino acid analyses. Their absolute stereochemistries were deduced by a combination of spectral and chemical studies. Micropeptins 88-A and 88-C to 88-F inhibited chymotrypsin potently with IC₅₀ of 0.4-10.0 µg/mL.