Abstract. Abstract Aim To assess the allelopathic effects of the submerged macrophyte Ceratophyllum demersum on four strains of phytoplankton species: two cyanobacteria (Microcystis aeruginosa - microcystin producing and M. panniformis - non-microcystin producing), and two chlorophytes (Ankistrodesmus falcatus and Raphidocelis subcapitata). Methods A coexistence experiment between C. demersum and the four strains was carried out for six days, with eight treatments and three replicates. The strains were cultivated in ASM1 culture medium, under controlled laboratory conditions. Two treatments were assigned for each strain, one with 6 g.L-1 of the macrophyte, and the control without the plant. Biomasses and growth rates of the strains were evaluated every two days, which were compared through the T-test and two-way ANOVA, respectively. Results The results varied among the strains, with toxic M. aeruginosa being intensely inhibited by C. demersum, with a decrease of 99.5% in its biomass (p<0.001), while non-toxic M. panniformis was less affected by the allelochemicals, with a reduction of 86.2% (p<0.001). Ankistrodesmus falcatus delayed its growth when in coexistence with the macrophyte, decreasing its biomass in 50.4% (p<0.01), while R. subcapitata was not altered (p>0.05). In coexistence with C. demersum, M. aeruginosa exhibited the lowest growth rates (-0.65 d-1), followed by M. panniformis (-0.15 d-1), A. falcatus (0.19 d-1), and R. subcapitata (0.34 d-1), with significant differences between all strains (p<0.001). Microcystis aeruginosa presented higher inhibition rates than M. panniformis (p<0.001), as well as, A. falcatus was more inhibited than R. subcapitata (p<0.05). Conclusions The presence of microcystins could influence the allelopathic responses of C. demersum, that may release more allelochemicals in coexistence with toxic strains of M. aeruginosa. Accordingly, C. demersum can be used in biomanipulation strategies to control toxic and non-toxic cyanobacterial blooms, without damaging other phytoplankton species, like chlorophytes.