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 of biological communities inter alia. It is now a defining time to assess the use of drones for these types of applications over natural areas and protected areas. UAV missions are increasing but most of them are just testing its 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 is aimed at collecting UAV applications contributing to a better understanding of biodiversity and ecosystem status, threats, changes and trends. Submissions were welcomed from purely scientific missions to operational management missions, evidencing the enhancement of knowledge in: Essential biodiversity variables and ecosystem services mapping; ecological integrity parameters mapping; long-term ecological monitoring based on UAVs; 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, ecosystem structure and processes assessment by using UAVs, mapping threats, vulnerability and conservation issues of biological communities and species; mapping of phenological and temporal trends and habitat mapping; monitoring and reporting of conservation status.