Abstract. This study compares the CO2 exchange of a natural bog forest, and of a bog drained for forestry in the pre-alpine region of southern Germany. The sites are separated by only ten kilometers, they share the same formation history and are exposed to the same climate and weather conditions. In contrast, they differ in land use history: at the Schechenfilz site a natural bog-pine forest (Pinus mugo rotundata) grows on an undisturbed, about 5 m thick peat layer; at Mooseurach a planted spruce forest (Picea abies) grows on drained and degraded peat (3.4 m). The net ecosystem exchange of CO2 (NEE) at both sites has been investigated for two years (July 2010 to June 2012), using the eddy covariance technique. Our results indicate that the drained, forested bog at Mooseurach is a much stronger carbon dioxide sink (−130 ± 31 and −300 ± 66 g C m−2 a−1 in the first and second year respectively) than the natural bog forest at Schechenfilz (−53 ± 28 and −73±38 g C m−2 a−1). The strong net CO2 uptake can be explained by the high gross primary productivity of the spruces that over-compensates the two times stronger ecosystem respiration at the drained site. The larger productivity of the spruces can be clearly attributed to the larger LAI of the spruce site. However, even though current flux measurements indicate strong CO2 uptake of the drained spruce forest, the site is a strong net CO2 source, if the whole life-cycle, since forest planting is considered. We determined the difference between carbon fixation by the spruces and the carbon loss from the peat due to drainage since forest planting. The estimate resulted in a strong carbon release of +156 t C ha−1 within the last 44 yr, means the spruces would need to grow for another 100 yr, at the current rate, to compensate the peat loss of the former years. In contrast, the natural bog-pine ecosystem has likely been a small but consistent carbon sink for decades, which our results suggest is very robust regarding short-term changes of environmental factors.