UAS have great potential to be used in a wide variety of civil applications such as environmental applications, emergency situations, surveillance tasks and more. The development of Flight Control Systems (FCS) coupled with the availability of other Commercial Off-The Shelf (COTS) components is enabling the introduction of Unmanned Aircraft Systems (UAS) into the civil market. Despite the increasing number of COTS components becoming available, much effort is still required in order to make UAS a viable commercial solution for civil applications. We believe that for UAS to be successful in this context they must be flexible systems able to perform a wide variety of missions with minimal reconfiguration and reduced operational costs. In previous work, a flight plan specification formalism and its corresponding execution engine have been presented. These elementsmay suffice for simple applications but for more complex scenarios, we need a mechanism that specifies the vehicle behavior not only in flight plan terms but also taking into account payload operation. To provide this integration and, at the same time, increase the level of automation a mission management layer is added on top of the flight plan management facilities. The system flexibility requirement is satisfied by decoupling the mission description from its execution engine. This paper introduces an XML based mission specification mechanism for modeling the event-driven state-based behavior of the UAS. The Mission Manager is the software module responsible for its execution. The integration of the Mission Manager with other components that form part of our UAS distributed architecture is also described.