To learn more whether toxin formation by cyanobacteria is controlled by quorum sensing, the concentrations of microcystins and of homoserine lactones have been followed during a summer period in the deep mesotrophic Lake Zürich and in the shallow eutrophic Lake Muzzano. Specific cyanobacterial populations are present in both lakes, Planktothrix rubescens dominates in Lake Zürich, Microcystis wesenbergii in Lake Muzzano. Both organisms produced microcystins, and homoserine-lactones were detected as well in most of the samples. However, no clear relation between the concentrations of the two compounds was observed with sampling intervals of 2 weeks.