Toxic cyanobacteria can affect several organisms, including herbivorous zooplankton, as cladocerans. In this study we tested the hypothesis that cladoceran species of different body size, origin and degree of exposure to toxic cyanobacteria would respond differently to a saxitoxin(STX)-producing strain of the cyanobacterium Cylindrospermopsis raciborskii (CYRF-01). Newborns were exposed to increasing concentrations of the strain CYRF-01 mixed to a fixed proportion of green algae for 14 days and survivorship, age at first reproduction, clutch size, total offspring and the intrinsic rate of population increase (r), as a measure of fitness, were estimated. Different responses to the strain CYRF-01 were observed, with Daphnia similis (temperate, large size) being more sensitive, followed by Moina micrura (tropical, small size), both presenting symptoms of decreased fitness and paralysis. While Ceriodaphnia richardi (tropical, small size) D. gessneri (tropical, medium size) and Diaphanosoma spinulosum (tropical, small size) showed neither of these symptoms, the later species showed even increased fitness in the cyanobacterial treatments relative to control with green algae, suggesting not only a greater resistance to this strain, but also that it can serve as a nutritional supplement for this cladoceran. In conclusion, the results showed that while some cladocerans species may be negatively affected in their fitness, others may be not affected at all or even utilize STX-producer cyanobacteria as a complementary resource. This suggests that responses of cladocerans to toxic cyanobacteria in nature may vary with species and that the presence of toxic cyanobacteria may shape zooplankton communities to the dominance of more tolerant herbivorous species.