A marine vessel running controlling apparatus controls running of a marine vessel and includes a pair of propulsion systems which respectively generate propulsive forces on a rear port side and a rear starboard side of a hull, and a pair of steering mechanisms which respectively change steering angles defined by directions of the propulsive forces with respect to the hull. The apparatus includes a target combined propulsive force acquiring section, a target movement angle acquiring section, a steering controlling section which controls the steering angles of the respective steering mechanisms such that a turning angular speed of the hull is substantially equal to a predetermined target angular speed, a target propulsive force calculating section which calculates target propulsive forces to be generated from the respective propulsion systems based on the target combined propulsive force, the target movement angle and the steering angles of the respective steering mechanisms, and a propulsive force controlling section which controls the respective propulsion systems so as to attain the target propulsive forces.