A marine vessel control system includes a control unit, a first communication bus, a second communication bus, and an auxiliary device connection section. The control unit includes a main output section arranged to output marine vessel maneuvering control information including starting information of a marine vessel propulsion device, and a sub output section arranged to output backup information including the starting information of the marine vessel propulsion device. The first communication bus is connected to the marine vessel propulsion device and the control unit, and is arranged to transmit the marine vessel maneuvering control information to the marine vessel propulsion device. The second communication bus is connected to the marine vessel propulsion device and the control unit, and is arranged to transmit the backup information to the marine vessel propulsion device. The second communication bus includes an auxiliary device connection section that is arranged to enable connection of an auxiliary device that executes communication, related to auxiliary information other than the marine vessel maneuvering control information, with at least one of the marine vessel propulsion device and the control unit via the second communication bus.