A power supply system for a watercraft propulsion device which ensures stable power supply to operating devices in the watercraft propulsion device. The power supply system for a watercraft propulsion device preferably includes an operating-system drive control circuit for driving and controlling operating mechanisms in the watercraft propulsion device and a battery for supplying power to the operating mechanisms via a power source circuit. The power source circuit preferably includes a plurality of separate independent batteries that are connected to the power source circuit, and a power supply control circuit is provided to supply power to the operating mechanisms using one of the batteries to be selected according to both battery conditions.