In a system for controlling outboard motors each mounted on a boat and each having an engine, a steering mechanism, a shift mechanism, an actuator driving at least one of the steering mechanism, the shift mechanism and a throttle valve of the engine, and a controller controlling operation of the actuator, comprising: a steering wheel operable by an operator; a shift/throttle lever operable by the operator; and a manipulated variable detector producing an output indicative of manipulated variable of at least one of the steering wheel and the shift/throttle lever; the manipulated variable detector being separately connected to each of the controllers in the outboard motors through an electric signal line to send the output to the controllers. With this, it becomes possible to control the operation of the actuators in the outboard motors separately for the individual outboard motors with simple structure without identifying the respective outboard motors.