Summary Microcystis is a cosmopolitan genus of cyanobacteria and occurs in many different forms. Large surface blooms of the cyanobacterium are well known in eutrophic lakes throughout the globe. We evaluated the role of microcystins (MCs) in promoting and maintaining bloom‐forming cell aggregates at environmentally relevant MC concentrations (0.25–10 µg l−1). MCs significantly enhanced Microcystis colony sizes. Colonial diameters in microcystin‐RR (MC‐RR)‐treated cultures (at 1 µg l−1) were significantly larger than control colonies, by factors of 1.5, 2.6 and 2.7 in Microcystis wesenbergii DC‐M1, M. ichthyoblabe TH‐M1 and Microcystis sp. FACHB1027 respectively. Depletion of extracellular MC concentrations caused Microcystis colony size to decrease, suggesting that released MCs are intimately involved in the maintenance of Microcystis colonial size. MC‐RR exposure did not influence Microcystis growth rate, but did significantly increase the production of extracellular polysaccharides (EPS). In addition, MC‐RR exposure appeared to trigger upregulation of certain parts of four polysaccharide biosynthesis‐related genes: capD, csaB, tagH and epsL. These results strongly indicate that induction of polysaccharides by MC‐RR was the major mechanism through which MCs enhanced colony formation in Microcystis spp. Cellular release of MCs, therefore, may play a key role in the persistence of algal colonies and the dominance of Microcystis.