An indirect adaptive control for an autonomous underwater vehiclemanipulator system (UVMS) based on an extended Kalman filter (EKF) is presented in this paper. This method overcomes the disadvantages of existing disturbance observers and direct adaptive control schemes, which are designed or analyzed by linear system techniques and regressor-based techniques. The proposed control scheme can be applied to UVMS' for various purposes such as payload compensation, interaction effects compensation, underwater current or external disturbance compensation and independent system control. The performance of the proposed controller is demonstrated numerically by the payload compensation and disturbance (underwater current) compensation for an UVMS consisting of a six degrees of freedom (6-DOF) underwater vehicle and a 3-DOF underwater manipulator. Copyright © 2012 by the International Society of Offshore and Polar Engineers (ISOPE).