This paper presents a robust position tracking control scheme for underwater vehicles moving in a vertical plane. The idea comes from the demand of underwater position tracking control for the newly borne Trans-media Aerial Underwater Vehicle (TMAUV). Although position control of a TMAUV is still within the scope of autonomous underwater vehicles (AUVs) control, it has new features. An underwater reference path for the TMAUV could be characterized by a strong maneuver that many assumptions in the conventional AUV controller design could not be employed. In this paper, a Lyapunov-based backstepping controller is developed for a nonlinear coupled input system releasing all constraints on the pitch angle, heave velocity, and angular velocity. Furthermore, neural networks and parameter estimation are employed to develop a robust controller in the presence of model uncertainties, parameter uncertainties, and external disturbances. This paper also solves the problem of adaptive estimation for the system parameters under the coupled input condition. Simulations are presented to demonstrate the feasibility and effectiveness. INDEX TERMS TMAUV, position tracking control, adaptive control, backstepping method.