This thesis describes the design, control and testing of the Ranger Neutral Buoyancy Vehicle flight control system. Chapter 1 provides the background of the vehicle and controllers used, along with this overview. Chapter 2 covers the details of the vehicle systems related to flight control. The thruster and buoyancy compensation system are described and characterized, and the sensor systems used do determine the vehicle state are described. The chapter ends with a description of the data management system. Chapter 3 describes the flight control operator interface. Interfaces for many vehicle functions are described, including controller selection and tuning, trajectory control, simulation, data recording, and analysis. Chapter 4 describes the vehicle dynamic model which is used both in the controller, and vehicle simulations. Next, the methods chosen for describing its attitude and angular velocity are described. This is followed by a discussion of the methods used for turning the raw sensor outputs into an estimate of vehicle attitude and angular velocity, followed by a description of estimator inaccuracies. Three controllers are then presented. A quaternion based PD controller commands the vehicle motion based on the current attitude and angular velocity error. The next controller adds nonlinear compensation by using a model of the system dynamics to compute the torque necessary to autonomously follow the specified trajectory. Finally, an adaptive controller is presented that uses observations of the vehicle behavior to update its estimates of the vehicle dynamic parameters. This is followed by a discussion of the hardware in the loop vehicle flight simulator and its performance compared with actual vehicle results. This section ends with a discussion of the trajectory generation system and a description of the vehicle auto balance algorithm. The experimental results section describes the initial tuning of the controllers and evaluation of their performance.