Three-year-old seedlings of black alder (Alnus glutinosa (L.) Gaertn.), a common European wetland tree species, were grown in native soil taken from an alder swamp. Fluxes of methane (CH4) and nitrous oxide (N2O) between the tree stem and the atmosphere were determined under controlled conditions. Both CH4 and N2O were emitted through the bark of the stem into the atmosphere when the root zone exhibited ‘higher-than-ambient’ CH4 and N2O gas mixing ratios. Flooding of the soil caused a decreased N2O emission but an increased CH4 efflux from the stem. Immediately after flooding of the soil, N2O was emitted from the seedlings’ bark at a rate of 350 μmol N2O m−2 h−1 whereas CH4 flux could not be detected. After more than 40 days of flooding CH4 fluxes up to 3750 μmol CH4 m−2 h−1 from the stem were measured, while N2O emission had decreased below the limit of detection. Gas efflux decreased with increasing stem height and correlated with gas mixing ratios in the soil, indicating diffusion through the aerenchyma as the major path of gas transport. From these results it is assumed that woody species with aerenchyma can serve as conduits for soil-derived trace gases into the atmosphere, to date only shown for herbaceous plants. This, yet unidentified, ‘woody plant pathway’ contributes to the total greenhouse gas source strength of wetlands.