Cyanobacteria are known for being inadequate as a food source for zooplankton, whether by their toxicity, large size, lack of essential compounds or due to feeding inhibitors. In eutrophic systems, however, higher abundance of rotifers is often observed with higher abundance of cyanobacteria, which indicates that not all cyanobacteria inhibit rotifer growth. We therefore hypothesized that the worldwide expanding cyanobacterium Cylindrospermopsis raciborskii is less harmful to the rotifer Brachionus calicyflorus than the worldwide occurring cyanobacterium Microcystis aeruginosa, based on the literature and field observations. Brachionus was exposed to Microcystis and Cylindrospermopsis in 2-day life-cycle assays in which multiple broods are produced and F1 generation can also reproduce. Use of different mixtures with a good food source (green alga) investigated potential nutritional inadequacy, and the influence of morphology or taste was tested in short-term grazing assays. Results showed that Brachionus was capable of ingesting both Cylindrospermopsis and Microcystis. Similar rates of ingestion of both cyanobacteria were observed, although diets consisting only of Microcystis did not support growth, whereas growth was supported by diets consisting only of Cylindrospermopsis. Mixing both cyanobacteria with the green alga also supported Brachionus growth, despite the toxins. Results corroborated our hypothesis that Cylindrospermopsis is less harmful to Brachionus than Microcystis. Moreover, it is in agreement with observations from a eutrophic tropical reservoir, where the zooplankton community (mainly abundance of rotifers) decreased during Microcystis blooms, whereas a diverse zooplankton community was established during periods of Cylindrospermopsis dominance.