A manipulation system includes: a manipulator that operates a microscopic object; a first input unit that generates a first movement command signal for moving the manipulator to a manipulator position corresponding to an input operation position; and a second input unit that generates a second movement command signal for moving the manipulator to a manipulator stored position stored in a storage. When the input operation position of the first input unit is a predetermined input operation position, the manipulator is enabled to be moved by an operation of the first input unit, or the manipulator is enabled to be moved by an operation of the second input unit.