Abstract. Peatlands are interesting as a carbon storage option, but are also natural emitters of the greenhouse gas methane (CH 4 ). Phragmites peatlands are particularly interesting due to the global abundance of this wetland plant (Phragmites australis) and the highly efficient internal gas transport mechanism, which is called humidity-induced convection (HIC). The research aims were to (1) clarify how this plant-mediated gas transport influences the CH 4 fluxes, (2) which other environmental variables influence the CO 2 and CH 4 fluxes, and (3) whether Phragmites peatlands are a net source or sink of greenhouse gases. CO 2 and CH 4 fluxes were measured with the eddy covariance technique within a Phragmites-dominated fen in southwest Germany. One year of flux data (March 2013-February 2014 shows very clear diurnal and seasonal patterns for both CO 2 and CH 4 . The diurnal pattern of CH 4 fluxes was only visible when living, green reed was present. In August the diurnal cycle of CH 4 was the most distinct, with 11 times higher midday fluxes (15.7 mg CH 4 m −2 h −1 ) than night fluxes (1.41 mg CH 4 m −2 h −1 ). This diurnal cycle has the highest correlation with global radiation, which suggests a high influence of the plants on the CH 4 flux. But if the cause were the HIC, it would be expected that relative humidity would correlate stronger with CH 4 flux. Therefore, we conclude that in addition to HIC, at least one additional mechanism must be involved in the creation of the convective flow within the Phragmites plants. Overall, the fen was a sink for carbon and greenhouse gases in the measured year, with a total carbon uptake of 221 g C m −2 yr −1 (26 % of the total assimilated carbon). The net uptake of greenhouse gases was 52 g CO 2 eq. m −2 yr −1 , which is obtained from an uptake of CO 2 of 894 g CO 2 eq. m −2 yr −1 and a release of CH 4 of 842 g CO 2 eq. m −2 yr −1 .