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 10 km, they share the same soil 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 ssp. 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 2 years (July 2010-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 44-year old spruces that over-compensates the two-times stronger ecosystem respiration a ... mehrt the drained site. The larger productivity of the spruces can be clearly attributed to the larger plant area index (PAI) 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 when the whole life-cycle since forest planting is considered. It is important to access this result in terms of the long-term biome balance. To do so, we used historical data to estimate the difference between carbon fixation by the spruces and the carbon loss from the peat due to drainage since forest planting. This rough estimate indicates a strong carbon release of +134 t C ha-1 within the last 44 years. Thus, the spruces would need to grow for another 100 years at about the current rate, to compensate the potential peat loss of the former years. In contrast, the natural bog-pine ecosystem has likely been a small but stable carbon sink for decades, which our results suggest is very robust regarding short-term changes of environmental factors.