Micropeptins C (1), D (2), E (3), and F (4) have been isolated from the freshwater cyanobacterium Microcystis aeruginosa (NIES-100). The structures were elucidated by analyses of MS, NMR spectra, and chemical degradation. Micropeptins C, D, E, and F inhibited chymotrypsin with IC(50)'s of 1.1, 1.2, 1.0, and 1.5 microg/mL, respectively.