Addressing ecological and evolutionary processes explaining biodiversity patterns is essential to identify the mechanisms driving community assembly. In the case of bacteria, the formation of new ecologically distinct populations or ecotypes is proposed as one of the main drivers of diversification. New ecotypes arise when mutation in key functional genes or acquisition of new metabolic pathways by horizontal gene transfer allow the population to exploit new resources, making possible their coexistence with parental population. Recently, we have reported the presence of toxic, microcystin-producing organisms from the Microcystis aeruginosa complex (MAC) through a wide environmental gradient (800 km) in South America, ranging from freshwater to estuarine-marine waters. In order to explain this finding, we hypothesize that the success of toxic organisms of MAC in such array of environmental conditions is due to the existence of ecotypes having different environmental preferences. So, we analysed the genetic diversity of microcystin-producing populations of Microcystis aeruginosa complex (MAC) by qPCR and high resolution melting analysis (HRMA) of a functional gene (mcyJ, involved in microcystin synthesis) and explored its relationship with the environmental conditions through the gradient by functional classification and regression trees (fCART). Six groups of mcyJ genotypes were distinguished and selected by different combinations of water temperature, conductivity and turbidity, determining the environmental preferences of each group. Since these groups were based on the basis of similar sequence and ecological characteristics they were defined as ecotypes of toxic MAC. Taking into account that the role of microcystins in MAC biology and ecology has not yet been elucidated, we propose that the toxin might have a role in MAC fitness that would be mainly controlled by the physical environment in a way such that the ecotypes that thrive in the riverine zone of the gradient would be more stable and less influenced by salinity fluctuations than those living at the marine limit of the estuary. These would periodically disappear or being eliminated by salinity increases, depending on the estuary dynamics. Thus, ecotypes generation would be an important mechanism allowing toxic MAC adapting to and succeed in a wide array of environmental conditions.