Toxic effects of freshwater cyanobacteria on mesozooplankton partially depend on the feeding strategies, generalist (cladocera) or selective filter-feeders (copepod) and on the type of toxin. Blooms of Cylindrospermopsis raciborskii (Nostocales) are increasingly more common in freshwaters. It can produce neurotoxins (paralytic shellfish poison, PSP), particularly in warm regions of the Americas. The knowledge about the effects of these neurotoxins on the clearance rate of zooplankton from warm regions still lags behind that of other world regions. We compared the toxin profile (using HPLC), morphology and growth rates of two PSP-producing C. raciborskii strains from South America. We evaluated the effect of these two strains on the clearance rate of two medium-sized grazers typical from subtropical and tropical environments, the copepod Notodiaptomus iheringi (~1.1 mm) and the cladoceran Daphnia pulex (~0.8 mm) in 2.5 h experiments. We found differences in the PSP profile, toxicity and morphology of the two C. raciborskii strains. Medium-sized predators were able to remove filaments of both strains in a similar amount despite their morphological and toxin differences. However, cladocera were significantly more affected than copepods in their clearance rates, suggesting differential consequences for their survival and success in warm freshwaters.