Three new protease inhibitors, micropeptins SF909 (t) and SF995 (2) and microcin SF608 (3), were isolated from the hydrophilic extract of a microcystis sp. waterbloom. The planar structure of compounds 1-3 was determined by homonuclear and inverse-heteronuclear 2D-NMR techniques as well as high-resolution mass spectrometry. The absolute configuration of the asymmetric centers was studied using Marfey's method for HPLC. Micropeptin SF909 (1) inhibited chymotrypsin with IC50 of 4.0 μg/mL while micropeptin SF995 (2) and microcin SF608 (3) inhibited trypsin with IC50's of 0.2 and 0.5 μg/mL, respectively.