A proof of concept study was performed to demonstrate the capabilities of quadrocopter air sampling for analysing the methane isotopic composition in the laboratory. Boundary layer mixing processes and the methane isotopic composition were studied with a quadrocopter system at Polder Zarnekow in Mecklenburg-West Pomerania in the North East of Germany, which has become a strong source of biogenically produced methane after rewetting the drained and degraded peatland. Methane 5 fluxes are measured continuously at the site. They show high emissions from May to September, and a strong diurnal variability with maximum methane fluxes up to 2 µmol m −2 s −1 for summer 2018. For two case studies on 23 May 2018 and 5 September 2018, vertical profiles of temperature and humidity were recorded up to an altitude of 650 m and 1000 m, respectively, during the morning transition. Air samples were taken at different altitudes and analysed in the laboratory for methane isotopic composition. The values showed a different isotopic signature in the vertical distribution during stable conditions in 10 the morning (-51.5 ‰ below the temperature inversion at an altitude of 150 m on 23 May 2018 and at an altitude of 50 m on 5 September 2018, -50.1 ‰ above). After the onset of turbulent mixing, the isotopic signature was the same throughout the vertical column with a mean value of -49.9 ± 0.45 ‰. During the September study, water samples were analysed as well for methane concentration and isotopic composition in order to provide a link between surface and atmosphere. The water samples reveal high variability on scales of few 10 m for this particular case. The airborne sampling system and consecutive analysis 15 chain were shown to provide reliable and reproducible results for two samples obtained simultaneously. The method presents a powerful tool for constraining the origin of methane by analysing its isotopic signature, and for measuring the vertical distribution of methane isotopic signature, which is based on mixing processes of methane within the atmospheric boundary layer.