The AUV (autonomous underwater vehicle) of the University of Canterbury targets to discover any foreign organisms residing on the sea chests of ships, which cause a risk for the domestic biodiversity, and removes them. With the design of the AUV finished, the primary goal of this paper is to design control software that stabilizes the vehicle and minimizes the error in the desired trajectory. The dynamical model with implemented assumptions ultimately leads to a decoupled
system of non-linear equations in three directions: surge, heave and yaw. For this system, experiments are designed (but not yet successfully accomplished) to identify the system parameters. With respect to control, a feedback linearization is firstly applied to a 1D case, which results in a satisfactory PIDcontroller, taking into account parameter perturbation and noise contamination. Finally, the under actuated problem in the 2D situation is evaluated, for which a path planning method and a state feedback control method is derived.