This study evaluates the toxicity of the Microcystis aeruginosa strain RST9501, isolated from Patos Lagoon, to cladocerans using standard tests with Ceriodaphnia dubia. The strain RST9501 was compared with the non-toxic M. aeruginosa strain NPJT-01. Chronic effects were estimated by evaluating reproduction and growth in C. dubia exposed to increasing concentrations of M. aeruginosa. Alternative food source constituted by Pseudokirchneriella subcapitata and Artemia chow was made available for all treatments. The presence of the two strains of M. aeruginosa inhibited both reproduction and growth in C. dubia. Also, regardless the presence of microcystin, there was an increase in toxicity as the cell concentration of both strains increased.