Large-scale production of microalgae for biofuels is often hampered by contamination of cultures with predators that feed on microalgae. An important group of predators are ciliates. Some species of marine microalgae in natural ecosystems are known to produce chemicals that act as deterrents against predators. In this study, we tested whether these chemicals (trans,trans-2,4-decadienal, dimethyl sulfoniopropionate (DMSP), glycine betaine and proline) as well as a chemical analogue (methyl 3-(methylthio)propionate or MMP) can be used to control contamination of cultures of the microalga Chlamydomonas by the predatory ciliate Sterkiella. All chemicals were capable of rapidly eradicating the ciliates from a contaminated Chlamydomonas culture, but at a higher dose also had a negative effect on the microalga. For each chemical an optimal dose was determined at which ciliates were controlled and losses in microalgal biomass productivity were minimized (0.13 mM decadienal, 4.75 mM DMSP, 10 mM MMP, 250–300 mM proline and 250–300 mM glycine betaine). In the case of DMSP, MMP and proline, biomass productivity was even the same as that of a non-contaminated culture. The chemicals were also effective against other ciliates (Stylonychia notophora, Oxytricha sp. and 2 different Paramecium species). These chemicals therefore have potential to be used as natural pesticides to control contamination of microalgal cultures by ciliates. Of all chemicals tested, DMSP and MMP are the most promising because they are effective at a relatively low dose and have a limited negative effect on microalgal productivity.