A new nonlinear disturbance observer-based tracking control scheme for an underwater manipulator is presented in this paper. This observer overcomes the disadvantages of existing disturbance observers, which are designed or analyzed by the linear system techniques. It can be applied in underwater manipulator systems 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 tracking control scheme is demonstrated numerically by the payload compensation and interaction effects compensation for a two degrees of freedom vertical underwater manipulator. © 2013 Taylor & Francis and The Robotics Society of Japan.