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In order to monitor and manage vessels in channels effectively, identification and tracking are very necessary. This work developed a maritime unmanned aerial vehicle (Mar-UAV) system equipped with a high-resolution camera and an Automatic Identification System (AIS). A multi-feature and multi-level matching algorithm using the spatiotemporal characteristics of aerial images and AIS information was proposed to detect and identify field vessels. Specifically, multi-feature information, including position, scale, heading, speed, etc., are used to match between real-time image and AIS message. Additionally, the matching algorithm is divided into two levels, point matching and trajectory matching, for the accurate identification of surface vessels. Through such a matching algorithm, the Mar-UAV system is able to automatically identify the vessel’s vision, which improves the autonomy of the UAV in maritime tasks. The multi-feature and multi-level matching algorithm has been employed for the developed Mar-UAV system, and some field experiments have been implemented in the Yangzi River. The results indicated that the proposed matching algorithm and the Mar-UAV system are very significant for achieving autonomous maritime supervision.