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Agriculture runoffs and discharge of wastewaters are the major causes of eutrophication. Although eutrophication could promote the thriving of any phytoplankter, harmful algal blooms (HABs) are dominated frequently by cyanobacteria. Currently, HABs dominated by the toxigenic cyanobacterium Microcystis aeruginosa in lakes and reservoirs are the main environmental concerns worldwide. This study aimed to determine how M. aeruginosa (Ma) modifies the population growth of Pseudokirchneriella subcapitata (Ps) and Ankistrodesmus falcatus (Af). Growth kinetics were determined for each species and in the combinations: Ps–Ma, Af–Ma, Af–Ps, and Ps–Af–Ma. At the end of experiments, photosynthetic pigments, phycobiliproteins, and microcystins were quantified. A logistic equation significantly described the growth trend for all of the tested species, enabling the identification of negative effects on early stages in the population growth of co‐cultures with the cyanobacterium; in addition, the interaction effects on the growth rate and in the maximum attainable population density were determined. The biomasses of A. falcatus and P. subcapitata were significantly higher when cultured individually than in all of the combinations with the cyanobacterium. The concentrations of chlorophyll a and b, as well as carotenoids, were lower in combined cultures, but phycobiliprotein content in the cultures with M. aeruginosa was not significantly affected. Microcystis aeruginosa negatively affected the growth of the microalgae, but A. falcatus was significantly more inhibited than P. subcapitata; however, microcystin concentrations were significantly reduced in the co‐cultures with microalgae. These results could help to explain the displacements of microalgae when cyanobacteria are present, giving rise to cyanobacterial blooms in eutrophic freshwaters. [ABSTRACT FROM AUTHOR]