While most experiments investigating zooplankton grazing on harmful cyanobacteria have been carried out with metazoan plankton, several protozoa can also feed efficiently on cyanobacteria. We investigated grazing by the mixotrophic flagellate Ochromonas sp. on the toxic cyanobacterium Microcystis aeruginosa. Ochromonas sp. grew rapidly on M. aeruginosa and had a strong impact on the population density of its prey. However, specific growth rates of Ochromonas sp. decreased over time, possibly indicating a negative impact on Ochromonas sp. mediated by M. aeruginosa. Grazing did not have any effect on the intracellular microcystin content of M. aeruginosa, and the ingested microcystins did not accumulate within Ochromonas sp. We studied the functional and numerical response of Ochromonas sp. grazing on the microcystin-producing strain M. aeruginosa PCC 7806 and its microcystin-deficient mutant. Ochromonas sp. showed a Type 3 functional response of very similar shape on both the toxic and non-toxic M. aeruginosa strain. Ingestion rates of Ochromonas sp. were even slightly higher on the toxic M. aeruginosa strain. We therefore found no indication of microcystins acting as a defence against mixotrophic flagellates.