The ciliate Euplotes vannus is a common protozoan in mass cultures of rotifers, and rapid reproduction of E. vannus occasionally reduces the rotifer yield. We performed a competition experiment between the rotifer Brachionus rotundiformis and the ciliate E. vannus. The ciliate was inoculated at three stages of the rotifer growth curve: the lag phase, the logarithmic growth phase and the stationary phase. When feeding on the alga Tetraselmis tetrathele, the ciliate increased and the rotifer growth was suppressed. The interference with rotifer growth was stronger in the lag and stationary phases than in the logarithmic growth phase. In contrast, when feeding on the alga Nannochloropsis oculata, the ciliate did not increase and the rotifer growth was similar to the control. In addition to the competition experiments, 15N incorporation experiments were performed on the ciliate to investigate its food preference. The nitrogen incorporation rates (% of body nitrogen h −1) of the ciliate were 0.7% through dead algae and 1.9% through rotifer feces when using T. tetrathele, and 0.4% through dead algae and 3.4% through rotifer feces when using N. oculata. The incorporation rate through bacteria-free rotifer feces was about one-third that of normal rotifer feces. These results indicated that the ciliate did not incorporate algal nitrogen directly, but rather through the microbial food chain, from phytoplankton to rotifer feces to bacteria. E. vannus incorporated the nitrogen of N. oculata and grew for a short time but the growth was soon suppressed. This growth inhibition may be due to allelopathy of N. oculata for E. vannus. Consequently, we propose that periodic addition of N. oculata should control E. vannus, and that this technique of applying allelopathy should be more sustainable than conventional treatments.