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Peatlands are interesting as a carbon storage option, but are also natural emitters of the greenhouse gas methane (CH₄). <i>Phragmites</i> peatlands are particularly interesting due to the global abundance of this wetland plant (<i>Phragmites australis</i>) 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 CH₄ fluxes, (2) which other environmental variables influence the CO₂ and CH₄ fluxes, and (3) whether <i>Phragmites</i> peatlands are a net source or sink of greenhouse gases. CO₂ and CH₄ fluxes were measured with the eddy covariance technique within a <span style="" class="text"><i>Phragmites</i></span>-dominated fen in southwest Germany. One year of flux data (March 2013–February 2014) shows very clear diurnal and seasonal patterns for both CO₂ and CH₄. The diurnal pattern of CH₄ fluxes was only visible when living, green reed was present. In August the diurnal cycle of CH₄ was the most distinct, with 11 times higher midday fluxes (15.7 mg CH₄ m⁻² h⁻¹) than night fluxes (1.41 mg CH₄ m⁻² h⁻¹). This diurnal cycle has the highest correlation with global radiation, which suggests a high influence of the plants on the CH₄ flux. But if the cause were the HIC, it would be expected that relative humidity would correlate stronger with CH₄ 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 <i>Phragmites</i> 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 CO₂ eq. m⁻² yr⁻¹, which is obtained from an uptake of CO₂ of 894 g CO₂ eq. m⁻² yr⁻¹ and a release of CH₄ of 842 g CO₂ eq. m⁻² yr⁻¹.