The effect of temperature on Ochromonas degrading microcystins was evaluated. High temperature favors Ochromonas to eliminate Microcystis. High temperature boosts Ochromonas to degrade microcystins. Both intracellular and extracellular microcystins can be degraded by Ochromonas. More extracellular microcystins were released at 20 °C than at higher temperatures.