We introduce a method for the determination of size distributions of natural Microcystis aeruginosa colonies. The analyses can be done on a routine basis with the (Eur)OPA flow cytometers. Colony sizes expressed as the number of mean single cells per colony are obtained using the ratio between the measured fluorescence per colony and the mean fluorescence of the single cells. The method is tested in three independent experiments. Several applications of this and similar analyses to cyanobacterial and phytoplanktonic studies and monitoring are discussed.