Abstract. This study presents an unoccupied aerial vehicle (UAV) platform used to resolve horizontal and vertical patterns of CO2 and CH4 mole fractions within the lower part of the atmospheric boundary layer. The obtained data contribute important information for upscaling fluxes from natural ecosystems over heterogeneous terrain and for constraining hot spots of greenhouse gas (GHG) emissions. This observational tool, therefore, has the potential to complement existing stationary carbon monitoring networks for GHGs, such as eddy covariance towers and manual flux chambers. The UAV platform is equipped with two gas analyzers for CO2 and CH4 that are connected sequentially. In addition, a 2D anemometer is deployed above the rotor plane to measure environmental parameters including 2D wind speed, air temperature, humidity, and pressure. Laboratory and field tests demonstrate that the platform is capable of providing data with reliable accuracy, with good agreement between the UAV data and tower-based measurements of CO2, H2O, and wind speed. Using interpolated maps of GHG mole fractions, with this tool we assessed the signal variability over a target area and identified potential hot spots. Our study shows that the UAV platform provides information about the spatial variability of the lowest part of the boundary layer, which to date remains poorly observed, especially in remote areas such as the Arctic. Furthermore, using the profile method, it is demonstrated that the GHG fluxes from a local sources can be calculated. Although subject to large uncertainties over the area of interest, the comparison between the eddy covariance method and UAV-based calculations showed acceptable qualitative agreement.