Here we present results from a field experiment in an Arctic wetland situated in Zackenberg, NE Greenland. During one growing season we investigated how dominance of the sedge Eriophorum scheuchzeri affected the below-ground concentrations of low molecular weight carbon compounds (LMWOC) and the fluxes of CO2 and CH4 in comparison to dominance of other sedges (Carex stans and Dupontia psilosantha). Three groups of LMWOC were analysed using liquid chromatography-ionspray tandem mass spectrometry, i.e., organic acids (OAs), amino acids (AAs) and simple carbohydrates (CHs). To identify the effect of plant composition the experiments were carried out in a continuous fen area with very little between species variation in environmental conditions, e.g., water-table and active layer thickness and soil temperature. The pool of labile LMWOC compounds in this Arctic fen was dominated by OAs, constituting between 75 and 83% of the total pore water pool of OAs, CHs and AAs. The dominant OA was acetic acid, an easily available substrate for methanogens, which constituted ≥85% of the OA pool. We estimated that the concentration of acetic acid found in pore water would support 2–2.5 h of CH4 flux and an additional continuous input of acetic acid through root exudation that would support 1.3–1.5 h of CH4 flux. Thus, the results clearly points to the importance of a continuous input for acetoclastic methanogenesis to be sustainable. Additionally, Eriophorum had a very strong effect on parts of the carbon cycle in the Arctic fen. The mean seasonal CH4 flux was twice as high in Eriophorum dominated plots, most likely due to a 1.7 times higher concentration of OAs in these plots. Further, the ecosystem respiration was 1.3 times higher in Eriophorum dominated plots. In conclusion, the results offer further support to the importance of certain vascular plant species for the carbon cycle of wetland ecosystems.