A propulsion system for a watercraft includes an engine. An air intake device delivers air to a combustion chamber. A throttle valve regulates an amount of the air. A control device sets the throttle valve to a desired position. A remote controller provides the control device with the desired position. The engine can include an auxiliary intake device that delivers supplemental air to the combustion chamber. A control valve normally shuts the supplemental air from the combustion chamber. The control device determines whether an abnormal condition occurs in setting the throttle valve to the desired position. The control device determines whether the amount of the air is insufficient. The control device controls the control valve to allow the supplemental air to move to the combustion chamber when the control device determines that the abnormal condition occurs and the amount of the air is insufficient.