The near-pristine bog ecosystems of Tierra del Fuego in southernmost Patagonia have so far not been studied in terms of their current carbon dioxide (CO2) sink strength. CO2 flux data from Southern Hemisphere peatlands are scarce in general. In this study, we present CO2 net ecosystem exchange (NEE) fluxes from two Fuegian bog ecosystems with contrasting vegetation communities. One site is located in a glaciogenic valley and developed as a peat moss-dominated raised bog, and the other site is a vascular plant-dominated cushion bog located at the coast of the Beagle Channel. We measured NEE fluxes with two identical eddy covariance (EC) setups at both sites for more than 2 years. With the EC method, we were able to observe NEE fluxes on an ecosystem level and at high temporal resolution. Using a mechanistic modeling approach, we estimated daily NEE models to gap fill and partition the half-hourly net CO2 fluxes into components related to photosynthetic uptake (gross primary production, GPP) and to total ecosystem respiration (TER). We found a larger relative variability of annual NEE sums between both years at the moss-dominated site. A warm and dry first year led to comparably high TER sums. Photosynthesis was also promoted by warmer conditions but less strongly than TER with respect to absolute and relative GPP changes. The annual NEE carbon (C) uptake was more than 3 times smaller in the warm year. Close to the sea at the cushion bog site, the mean temperature difference between both observed years was less pronounced, and TER stayed on similar levels. A higher amount of available radiation in the second observed year led to an increase in GPP (5 %) and NEE (35 %) C uptake. The average annual NEE-C uptake of the cushion bog (−122±76 gm−2a−1, n=2) was more than 4 times larger than the average uptake of the moss-dominated bog (−27±28 gm−2a−1, n=2).