Genetic and eco-physiological differences of South American Cylindrospermopsis raciborskii isolates support the hypothesis of multiple ecotypes

► The mechanisms underlying the success and expansion of the toxic cyanobacteria Cylindrospermopsis raciborskii are still unknown. ► In this work we studied the ecophysiology, genetic variability and molecular phylogeny of two isolates from Uruguay (South America). ► We found differences in ecological preferences, genetic background and phylogeny suggesting the existence of ecotypes whose success is subjected to the local environmental conditions.