Five new protease inhibitors, micropeptins SD944 (1), SD979 (2), SD999 (3) and SD1002 (4) and microginin SD755 (5) were isolated along with two known inhibitors, micropeptin SF995 (6) and microcin SF608 (7), from the hydrophilic extract of Microcystis aeruginosa. The planar structure of compounds 1±5 was determined by homonuclear and inverse-heteronuclear 2D-NMR techniques as well as high-resolution mass spectrometry. The absolute con®guration of the asymmetric centers was studied using Marfey's method for HPLC. Compounds 1±4, 6 and 7 are serine-protease inhibitors while compound 5 was found to inhibit amino-proteases. q 2001 Elsevier Science Ltd. All rights reserved.