This paper demonstrates a novel motion control approach for biomimetic underwater vehicles with pitching fins. Even though these vehicles are highly maneuverable, the actua-tion of their different degrees of freedom (DOFs) is strongly coupled. To address this problem, we propose to use smooth DOF prioritization depending on which maneuver the vehicle is about to do. DOF prioritization has allowed us to develop a modular, easily applicable and extendable motion control architecture for U-CAT vehicle, which is meant for archaeological shipwreck penetration. We demonstrate the benefits of this architecture by developing an remotely operated vehicle autopilot for depth and yaw using a nonlinear state feedback controller. We also show the extensibility of the approach by controlling 3 DOFs of a fully autonomous U-CAT. The real-time experimental results show high position tracking precision (depth RMS error: 1.9 cm; yaw RMS error: 2.5 •) Comparative experiments justify the use of DOF prioritization.