SUMMARYToxic microcystins from cyanobacteria belonging to the genus Microcystis have been responsible for the death of various animals. In batch culture experiments, pre‐dation and degradation characteristics of Microcystis viridis and its toxic metabolite, microcystin‐RR, were examined using the micro‐animals, Aeolosoma hempri‐chi and Philodina erythrophthalma combined with endemic aggregated bacteria isolated from a biofilm. Although M. viridis was favorably predated and decomposed by the two micro‐animals, the reduction of microcystin‐RR was relatively low compared to the culture with the animals in the presence of the mixed bacteria, where degradation of the toxin was enhanced under aerated conditions. The aerated bacteria could degrade the eluted toxin faster than in any other condition and an initial toxin concentration of above 40 μg L‐1 was completely degraded in 10 days. Furthermore, in a continuous bioreactor packed with biofilm carrier, a toxin level of 9.74 μg g‐1 in the inflow water was reduced by 94.0% at a hydraulic retention time of less than 12 h. Moreover, in a practical biofilm plant, a toxin concentration of 34.9 μg g‐1 was degraded at a short hydraulic retention time (HRT) of 2 h. The efficiency of toxin removal in the plant at the short HRT coincided with that of laboratory studies. It was considered that A. hemprichi and P. erythrophthalma contributed to the predation and decomposition of viable M. viridis cells, subsequently these released toxin which could be efficiently degraded by the aerated bacteria.