A marine vessel propulsion system includes port and starboard drive systems, each including an engine, an engine throttle, and a transmission furnishing drive power to a propeller on a drive shaft. Each transmission includes forward and reverse clutches, and each clutch can be fully engaged, fully disengaged and modulated. Two alternately usable separate control stations operate the throttles and clutches to control vessel speed and direction. Each control station comprises port and starboard sets of manually operable control devices, and each set includes a mode selector switch for selecting cruise mode or troll mode for its respective throttle and a manually operable direction/speed control lever. In troll mode the lever selects and modulates the selected respective clutch to control propeller speed. In cruise mode the lever fully engages the selected respective clutch and also regulates the engine throttle to control propeller speed. Port and starboard manually operable power-link function selector switches at each control station enable one direction/speed control lever to control both drive systems simultaneously in the forward cruise mode. Electronic controllers process control station output signals and feedback signals indicative of engine speeds and propeller direction and speeds and then provide drive system control signals. Transfer of control to one station from another is possible.