In this paper the system control design stages for an autonomous underwater vehicle are presented. The vehicle must be able to sail on sea surface, following a path without losing its route and once a position is reached, a dive following a perpendicular path to the surface is carried out. A two level system control are proposed. The primary level will control the navigation of the vehicle where a linear controllers are proposed. Whereas in secondary level guidance system, collision system, start, stop and abort mission events will be ordered by neuro-fuzzy control. The implementation of these algorithms will be supported by a Motorola Coldfire family microcontroller (MCF5272).