An aqueous MeOH extract of Microcystis aeruginosa (IL-399) afforded three new protease inhibitors, micropeptin HH978 (1), micropeptin HH960 (2), and micropeptin HH992 (3), as well as the known aeruginosin GH553 and microguanidine AL772. The structures of the compounds were elucidated using 1D and 2D NMR techniques, as well as high-resolution mass spectrometry. The absolute configurations of 1-3 were determined using Marfey's method for amino acid and chiral-phase HPLC for hydroxy acids. The inhibitory activity of the compounds was determined for the serine proteases trypsin, thrombin, elastase, and chymotrypsin. The structure elucidation and biological activities of the new natural products are discussed.