Unmanned aerial vehicles (UAVs), so-called 'drones', have been widely used to monitor wild animals. Here, we tested a UAV with red, green, and blue (RGB) and thermal cameras to detect free-living birds in a high Arctic region in North Greenland and in a restricted area in the Republic of Korea. Small flocks of molting pink-footed geese (Anser brachyrhynchus) near sea ice and incubating common ringed plovers (Charadrius hiaticula) in the Arctic environment were chosen for the RGB and thermal image studies. From the acquired images, we built mosaicked RGB images and coregistered thermal images, and estimated the animal shapes. Our results showed that geese were discriminated in both RGB and thermal images with water and sea ice backgrounds. Incubating plover bodies were not distinguished in RGB images due to their cryptic coloration, but they were detected in thermal images with cold background areas in the Arctic environment. We further conducted a blind survey in a restricted area under military control in Korea near the breeding sites of black-faced spoonbill (Platalea minor), which is an endangered species. From UAV flights with RGB and thermal cameras operated out of the restricted area, we acquired images of white objects in the mudflats and verified that the objects were resting spoonbills by watching the birds. We suggest that thermal cameras and UAVs can be applied to monitor animals in extreme environments and in restricted areas and help researchers find cryptic wader nests.