Modern developments in the fields of control, sensing, and communication have made increasingly complex and dedicated underwater robot systems a reality. Used in a highly hazardous and unknown environment, the autonomy and dynamics of the robots is the key to mission success. Though the dynamics of underwater vehicle system is highly coupled and non linear in nature, decoupled control system strategy is widely used for practical applications. As autonomous underwater vehicles need intelligent control systems, it is necessary to develop control systems that really take into account the coupled and non-linear characteristics of the system. In this paper, we propose a control system with a nonlinear control strategy that takes into account the above factors. So far, AUV dynamics has often been derived under various assumptions on the motion of the vehicle. However, such assumptions may induce large modelling errors and may cause severe control problems in many practical applications. We propose to use both Lyapunov and state space back stepping based non linear control to overcome the modelling errors. The strategy will be tested through simulations for a flat-fish type AUV. Basic controller design and the simulation results will be discussed in the paper. A comparison of the results for conventional method and the proposed method will also be presented. © 2008 IEEE.