1. In order to test the effect of Ochromonas sp., a mixotrophic chrysophyte, on cyanobacteria, grazing experiments were performed under controlled conditions. We studied grazing on three Microcystis aeruginosa strains, varying in toxicity and morphology, as well as on one filamentous cyanobacterium, Pseudanabaena sp. Furthermore, we analysed the co-occurrence of Ochromonas and Microcystis in natural systems in relation to various environmental parameters (TP, TN, DOC, temperature, pH), using data from 460 Norwegian lakes. 2. Ochromonas was able to feed on all four cyanobacterial strains tested, and grew quickly on all of them. The chrysophyte caused net growth reductions in all three Microcystis strains (the very toxic single-celled strain PCC 7806; the less toxic colony-forming Bear AC and the less toxic single-celled Spring CJ). The effect of Ochromonas was strongest on the Spring CJ strain. Although the effect of Ochromonas grazing on the growth of Pseudanabaena was relatively smaller, it also reduced the net 3. After 4 days of incubation with Ochromonas the total amount of cyanotoxins in the three Microcystis strains was reduced by 91.1–98.7% compared with the controls. 4. Ochromonas occurred in similar densities across all 460 Norwegian lakes. Microcystis occurred only at higher TN, TP, temperature and pH values, although its density was often several orders of magnitude higher than that of Ochromonas. Ochromonas co-occurred in 94% of the samples in which Microcystis was present. 5. From our study it is not clear whether Ochromonas could control Microcystis blooms in natural lakes. However, our study does demonstrate that Ochromonas usually occurs in lakes with Microcystis, and our small scale experiments show that Ochromonas can strongly reduce the biomass of Microcystis and its toxin content.