A marine vessel propulsion system includes a propulsive force generator to generate a propulsive force, a drive source to drive the propulsive force generator, and a controller configured or programmed to control the drive source to perform marine vessel maneuvering-related functions including at least one limited function. The controller includes an interface, and is further configured or programmed to include a restriction unit to restrict a control operation for the limited function, and a restriction cancellation unit to cancel the restriction effected by the restriction unit to permit the control operation for the limited function if a predetermined keycode is inputted from the interface or is registered in the controller.