This paper proposes an observer-assisted (indirect) adaptive trajectory tracking control scheme for an under-actuated autonomous underwater robotic vehicle. The proposed control algorithm was based on feedback linearization control, using the estimated vehicle (hydrodynamic) parameters and external disturbance parameters (e.g., underwater current, buoyancy variations, etc.). These parameters were estimated online by employing a well-known non-linear observer extended Kalman filter. Using these estimated parameters and estimated disturbance vector, a feedback linearization control system was constructed for an under-actuated underwater vehicle. The effectiveness of the proposed system demonstrated and discusses the robustness using simulation results. The simulation results were compared with those of a control scheme that employed true parameters and without compensation, as well and results show the proposed scheme works well. © 2013 ACM.