This paper proposes a new tracking controller for autonomous underwater vehicle-manipulator systems (UVMSs) using the concept of model reference adaptive control. It also addresses the detailed modeling and simulation of the dynamic coupling between an autonomous underwater vehicle and manipulator system based on Newton–Euler formulation scheme. The proposed adaptation control algorithm is used to estimate the unknown parameters online and compensate for the rest of the system dynamics. Specifically, the influence of the unknown manipulator mass on the control performance is indirectly captured by means of the adaptive control scheme. The effectiveness and robustness of the proposed control scheme are demonstrated using numerical simulations.