Harmful algal blooms are one of the greatest challenges when preserving water sources, especially when involving cyanobacteria such as Microcystis aeruginosa. Finding remediation possibilities is needed, and one of them has been the use of macrophytes such as the species Myriophyllum, which have presented allelopathic mechanisms of phytoplankton control. Thus, this work aimed to evaluate the inhibition of M. aeruginosa cell growth in a co-exposure with Myriophyllum aquaticum and the influence on microcystin-LR concentration. The experiments were carried out using a culture of M. aeruginosa (1x106 cells mL-1) in a co-exposure with M. aquaticum for seven days. The inhibitory effects were investigated by counting the cells; the effects on photosynthetic pigments were measured and microcystin-LR was quantified in the culture medium on the last experimental day. To evaluate the possible effects of competition for nutrients and space, the concentration of total orthophosphate was quantified and treatment with plastic plants was used. The experiments with Myriophyllum aquaticum achieved the total inhibition of M. aeruginosa growth and a significant reduction of the photosynthetic pigments (> 98%). Additionally, we observed a reduction of microcystin-LR concentration (79%) in the tests with macrophytes when compared to the control. Competition for space and nutrients was not observed, demonstrating that the effects on M. aeruginosa were caused by aquatic macrophyte presence. These results may indicate that M. aquaticum causes inhibitory effects on cyanobacteria growth by allelopathic effects and removes microcystin-LR.