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In this work the mission control and supervision system developed for the ROAZ Autonomous Surface Vehicle is presented. Complexity in mission requirements coupled with flexibility lead to the design of a modular hierarchical mission control system based on hybrid systems control. Monitoring and supervision control for a vehicle such as ROAZ mission is not an easy task using tools with low complexity and yet powerful enough. A set of tools were developed to perform both on board mission control and remote planning and supervision. "ROAZ-Mission Control" was developed to be used in support to bathymetric and security missions performed in river and at seas.