In a power supply system for a watercraft, a controller in a first state connects a first electric circuit to a third electric circuit to supply electric power from a first engine battery to an electric device, and disconnects a second electric circuit from the third electric circuit to charge a second engine battery by a second generator. In a second state, the controller connects the second electric circuit to the third electric circuit to supply the electric power from the second engine battery to the electric device, and disconnects the first electric circuit from the third electric circuit to charge the first engine battery by a first generator.