Mass growth of blue-green algae in eutrophic water bodies leads to a large amount of toxins, e.g. microcystins (MCs). How to remove MCs from water bodies is an environmental problem. In this study, an algicidal bacterium Ochrobactrum sp. FDT5 was isolated and found to have microcystin-LR (MC-LR) degradation capacity, which could be enhanced by a domestication process. The FDT5 cell density, MC-LR initial concentration, temperature, and pH on the degradation of MC-LR were investigated. The results indicated that the initial cell density of FDT5 and the initial concentration of MC-LR could influence MC-LR degradation. The optimum conditions were under the temperature of 35°C with pH of 7.0. After FDT5 was exposed to MC-LR for 2 days, FDT5 cells produced active cellular components that degraded MC-LR. These cellular components were heat-inactivated and removed when FDT5 cells were removed by filtration.