Microcystins (MCs) are cyanobacterial hepatotoxins responsible for animal poisonings and human health incidents. Whilst the colony-forming Microcystis spp. are among the most commonly encountered MC-producers, quantitative data are lacking on MC concentrations per colony and on the localization of MCs within Microcystis colonies. We have quantified and localized MCs in colonies of a laboratory strain of Microcystis aeruginosa using antibodies against microcystin-LR. MCs were quantified in 70 colonies of Microcystis EBRO. The MC quota per colony (n ¼ 70) ranged from 0.36 to 15.23 ng colony À1 and showed a positive relationship with colony size. MC distribution within the colonies was determined using cryosectioning and immunogold localization. MCs were specifically localized in the nucleoplasmic region of the cells and were also associated with major inclusion bodies, with a preferential association with the thylakoids (the most abundantly labelled subcellular site) and around polyphosphate bodies. All of the cells in the MC-containing colonies were specifically labelled for MCs with no gradients in MC antibody labelling across colony transects being apparent. The toxins were also found to be associated with colony mucilage. MC antisera are useful for the investigation of MC distribution within cyanobacterial populations by ELISA, and may be used in the future to localize the toxins within cyanobacterial colonies, filaments and gyres from natural environments.