This paper describes the characterization of proteases in Microcystis aeruginosa PCC7806 cells being inhibited by a metabolite produced by another Microcystis strain, Microcystis Ku1. With casein and oligopeptide substrates and specific inhibitors we detected activity similar to bacterial serine endoproteases. Substrate SDS-polyacrylamide gel electrophoresis revealed the presence of nine bands of proteases (ca. 35˜125 kDa). The cyanobacterial enzymes were insensitive to endogenous trypsin-inhibitory metabolites. Microcystis Ku1 produced a metabolite, tentatively characterized as microviridin, inhibiting both cyanobacterial proteases and trypsin at an estimated IC50 of, respectively, 2.2 and 9.0 μg mL-1. On activity gels, inhibitors specific to animal trypsin and elastase and the putative microviridin led to an inactivation of the proteases associated with the 88 and 110 kDa bands. We hypothesize that in Microcystis populations there is a “cross-talk” between the inhibitors and the proteases, and only the colonies of identical chemotypes can possibly aggregate to form blooms.