Methane is a very effective greenhouse gas, but the role of the Polar Regions in the methane budget and its sources there is subject to discussion. The sparse surface network data and satellite data indicate significant source regions above the polar oceans.The remotely piloted quadrocopter ALICE was developed for taking air samples to study methane isotopic composition related to different polar atmospheric boundary layer conditions above sea ice and open water (German Research Foundation, DFG, grant No. LA2907/8-1, DA 2907/5-1). Adapted to rough polar conditions the quadrocopter carries twelve 100 ml glass bottles for air sampling and sensors for air temperature, humidity, irradiation and surface temperature up to 1000 m above ground. The samples can be taken by opening the evacuated glass bottles at any point of the trajectory, at predefined positions or manually triggered by the operator. The quadrocopter is a tool to get vertical profiles of air samples easier than with other methods.The initially tested prototype was field operated for the first time during Polarstern cruise PS109 (ARK-XXXI/4) in September/October 2017. A scientific case study was done at rewetted peatland area at Zarnekow (Northeast Germany), by probing the atmosphere above this known methane source during the morning transition at one day in late spring 2018 and at one day in early autumn 2018 (Lampert et al., https://www.atmos-meas-tech-discuss.net/amt-2019-111/) The data set includes 5 flights of the initial operational field testing during the PS109 expedition and two days of surveying a rewetted peatland area at Zarnekow.In the PANGAEA data set, different parameters characterizing the measurement system, the meteorological conditions and the air sampling system are provided: Time of the measurements, coordinates and altitude of the quadrocopter based on global navigation satellite systems (GNSS) and barometric pressure, three-dimensional velocity of the quadrocopter, raw data of air temperature and humidity measured by several temperature and humidity sensors, surface temperature, upward and downward solar radiation, and the pressure inside the twelve glass bottles, to control at which altitude the sample was taken.For the Zarnekow data set, the methane isotopic composition of each sample is included, as well as the corresponding sampling altitude. Methane concentration and methane isotopic composition for additional water samples are provided in Lampert et al. (2019).