This paper presents the design and implementation of a mission control system for an AUV. The mission is easily described using an imperative-like pseudo-code that allows sequential/parallel, conditional/unconditional and iterative task execution. This pseudo-code is manually translated into a Petri net, to formally describe the mission thread of execution. Then the mission controller executes the Petri net in real-time on a behavioural control architecture enabling/disabling and configuring robot behaviours. The proposed system has been programmed and tested on a low cost AUV performing a simplified mission of scientific interest.