The method for treating microcystin-containing water which detoxifies microcystin in the microcystin-containing water, the method comprises the step of: bringing the microcystin-containing water into contact with a Sphingomonas bacterium to degrade biologically the microcystin in the microcystin-containing water, wherein: the Sphingomonas bacterium is a strain FERM P-19480 which is deposited as strain MDB1 with International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology.