ABSTRACTInformation about the annual carbon fluxes of fen and meadow ecosystems in alpine environments is rare. We studied the influence of photosynthetic active radiation (PAR), plant green area index (GAI), soil temperature, and water-filled pore space (wfps) on the net CO2 emission at four alpine sites (one meadow and three fen sites) differing in water balance and plant community. Measurements over two years were made in the Eastern Alps, Austria, including two snow-free periods and two snow periods. During snow-free periods, net CO2 gain during daylight periods (NEElight , PAR > 0) depended on PAR and GAI. The net CO2 emission rate at night (Rtot , PAR = 0) was positively related to soil temperature, while low wfps reduced the carbon loss via Rtot of the meadow and driest fen study site but reinforced carbon loss of the wetter fen sites. Daily average ecosystem net CO2 gain (NEEday ) during snow-free periods (averaged over both years) at the meadow was 3.5 g CO2 m−2 d−1 and ranged from 1.5 to 3.4 g CO2 m−2 d−1 at the fen sites. Mean average daily wintertime CO2 emission was low, being only −0.9 g CO2 m−2 d−1 for meadow and between −0.2 and −0.7 g CO2 m−2 d−1 for all fen sites. All sites function as significant annual net carbon sinks, with a net carbon gain from 50 to 121 g C m−2 a−1 (averaged over both years) irrespective of water balance. Our results indicate that these alpine fen sites that have built up a large carbon stock in the past do not gain a further carbon surplus compared with the meadow under the current climate.