In this paper a comparative analysis of Mamdani and Sugeno type fuzzy autopilots for ships is given. Both autopilots have two inputs: the heading signal and the yaw rate signal, and only one output: command rudder angle. Input variable fuzzification, fuzzy associative memory (FAM) rules, and output set defuzzification are described. The control system for the course-keeping composed of the nonlinear ship, the steering gear servo system, fuzzy autopilot and wave disturbance is described. Both autopilots are compared in three different sailing conditions: without wave disturbance, with wave disturbance and with wave disturbance and wave filtering. The notch filter was used for filtering of second-order wave disturbances. The influence of wave disturbance on course-keeping performance was analyzed. Even though the obtained performance in simulations are very similar, authors prefer Sugeno type fuzzy autopilot, due to less strain of the steering gear servo system and faster and more accurate heading obtained.