Abstract: A method and system provide for on-board localization in a unmanned aerial system (UAS). A map image if generated (using previously acquired images) of an area that the UAS is overflying. The map image is then processed by orthorectifying, referencing the map image in a global reference frame, and generating an abstract map by detecting features and locating the features in the global reference frame. The UAS is then localized by acquiring camera images during flight, selecting a subset of the camera images as localization images, detecting on-board image features (in the localization images), mapping features from the detected on-board image features to the abstract map, deleting outliers to determine an estimated 3D pose, and refining the 3D pose. The localized UAS then used to autonomously navigate the UAS.