This paper presents an optimized robust controller for trajectory control of an Autonomous Underwater Vehicle (AUV) - Manipulator system. The trajectory of a manipulator mounted on an AUV is highly affected by the dynamic coupling between the AUV and manipulator as well as the hydrodynamic parameter variations. Design of a controller to overcome these effects is presented. Unconstrained optimization method is used to optimize the parameters of the controller. Complete dynamics is modelled using bondgraph technique. Comparative error analysis with and without optimization parameters has been carried out. The results show that the designed optimized controller provides the high performance in trajectory tracking of the manipulator and reduces the average percentage error of manipulator trajectory by considerable amount. © 2010 IEEE.