The growing need for ocean surveillance and exploration has pushed the development of novel autonomous underwater vehicle (AUV) technology. A current trend is to make use of bio-inspired propulsor to increase the overall system efficiency and performance, an improvement that has deep implications in the dynamics of the system. The goal of this dissertation is to propose a generic robust control framework specific for bio-inspired autonomous underwater vehicles (BIAUV). These vehicles utilize periodic oscillation of a flexible structural component to generate thrust, a propulsion mechanism that can be tuned to operate under resonance and consequently improve the overall system efficiency. The control parameter should then be selected to keep the system operating in such a condition. Another important aspect is to have a controller design technique that can address the time-varying behaviors, structured uncertainties and system nonlinearities. To address these needs a robust, model-based, nonlinear controller design technique is presented, called digital sliding mode controller (DSMC), which also takes into account the discrete implementation of these laws using microcontrollers. The control law is implemented in the control of a jellyfish-inspired autonomous underwater vehicle. / Ph. D.