Micropeptins 88-N (1) and 88-Y (2), new 3-amino-6-hydroxy-2-piperidone (Ahp)-containing cyclic depsipeptides, were isolated from Microcystis aeruginosa NIES-88. The structures were elucidated by analyses of HRFABMS, 1D and 2D NMR spectra, and chemical degradation. Micropeptins 88-N and 88-Y inhibited chymotrypsin. The inhibitory activities were closely related to the amino acid residue that was attached to the amino group of Ahp.