Unmanned aerial vehicles (UAV) have already become an affordable and cost-efficient tool to quickly map a targeted area for many emerging applications in the arena of ecological monitoring and biodiversity conservation. Managers, owners, companies, and scientists are using professional drones equipped with high-resolution visible, multispectral, or thermal cameras to assess the state of ecosystems, the effect of disturbances, or the dynamics and changes within biological communities inter alia. We are now at a tipping point on the use of drones for these type of applications over natural areas. UAV missions are increasing but most of them are testing applicability. It is time now to move to frequent revisiting missions, aiding in the retrieval of important biophysical parameters in ecosystems or mapping species distributions. This Special Issue shows UAV applications contributing to a better understanding of biodiversity and ecosystem status, threats, changes, and trends. It documents the enhancement of knowledge in ecological integrity parameters mapping, long-term ecological monitoring based on drones, mapping of alien species spread and distribution, upscaling ecological variables from drone to satellite images: methods and approaches, rapid risk and disturbance assessment using drones, mapping albedo with UAVs, wildlife tracking, bird colony and chimpanzee nest mapping, habitat mapping and monitoring, and a review on drones for conservation in protected areas.