This report describes a rule based system that has been designed to oversee the maneuvering of the autonomous underwater vehicle, AUV II, that has been constructed at the Naval Postgraduate School. The system will monitor the progress from the AUV launch point to a goal area and back to the origin. It is able to make informed decisions about the mission, taking into account the navigational path, the vehicle subsystems health, the sea environment, and the specific mission profile which is downloaded from an off-board mission planner. Heuristics for maneuvering, avoidance of uncharted obstacles, waypoint navigation, and reaction to emergencies - essentially the expert knowledge of a submarine captain - have been coded using the expert system shell CLIPS. The design of a high level control software architecture for AUV II and the development of the domain specific knowledge for AUV operation are discussed in detail. Simulation results showed that the system is capable of reacting to various adverse situations in a timely manner. Expert Systems Autonomous Underwater Vehicle Rule Based Control, Mission Execution