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Herbivory is an important part of most ecosystems and affects the ecosystems' carbon balance both directly and indirectly. Little is known about herbivory and its impact on the carbon balance in high arctic mire ecosystems. We hypothesized that trampling and grazing by large herbivores influences the vegetation density and composition and thereby also the carbon balance. In 2010, we established fenced exclosures in high arctic Greenland to prevent muskoxen (Ovibos moschatus) from grazing. During the growing seasons of 2011 to 2013 we measured CO₂ and CH₄ fluxes in these ungrazed blocks and compared them to blocks subjected to natural grazing. Additionally, we measured depth of the water table and active layer, soil temperature, and in 2011 and 2013 an inventory of the vegetation density and composition were made. In 2013 a significant decrease in total number of vascular plant (33–44%) and Eriophorum scheuchzeri (51–53%) tillers were found in ungrazed plots, the moss-layer and amount of litter had also increased substantially in these plots. This resulted in a significant decrease in net ecosystem uptake of CO₂ (47%) and likewise a decrease in CH₄ emission (44%) in ungrazed plots in 2013. While the future of the muskoxen in a changing arctic is unknown, this experiment points to a potentially large effect of large herbivores on the carbon balance in natural Arctic ecosystems. It thus sheds light on the importance of grazing mammals, and hence adds to our understanding of natural ecosystem greenhouse gas balance in the past and in the future.