Vegetation and hydrology are important controlling factors in peatland methane dynamics. This study aimed at investigating the role of vegetation components, sedges, dwarf shrubs, and Sphagnum mosses, in methane fluxes of a boreal fen under natural and experimental water level drawdown conditions. We measured the fluxes during growing seasons 2001–2004 using the static chamber technique in a field experiment where the role of the ecosystem components was assessed via plant removal treatments. The first year was a calibration year after which the water level drawdown and vegetation removal treatments were applied. Under natural water level conditions, plant-mediated fluxes comprised 68 %–78 % of the mean growing season flux (1.73±0.17 g CH4 m−2 month−1 from June to September), of which Sphagnum mosses and sedges accounted for one-fourth and three-fourths, respectively. The presence of dwarf shrubs, on the other hand, had a slightly attenuating effect on the fluxes. In water level drawdown conditions, the mean flux was close to zero (0.03±0.03 g CH4 m−2 month−1) and the presence and absence of the plant groups had a negligible effect. In conclusion, water level acted as a switch; only in natural water level conditions did vegetation regulate the net fluxes. The results are relevant for assessing the response of fen peatland fluxes to changing climatic conditions, as water level drawdown and the consequent vegetation succession are the major projected impacts of climate change on northern peatlands.