Two novel biologically active short peptides, aeruginosins KY642, KY608 and the known aeruginosin 98A were isolated from the cyanobacterium Microcystis sp. strain (IL-323), which was collected from a water reservoir near Kfar-Yehoshua, Valley of Armageddon, Israel. Aeruginosins KY642, KY608 and 98A are linear modified peptides containing four building blocks, one of which is the modified amino acid, Choi (2-carboxy-6-hydroxyoctahydroindole). Aeruginosin KY642 and aeruginosin KY608 inhibit the activity of the photolytic enzyme trypsin with IC50 of 1.4 and 1.7 mg/mL, respectively.