Carbon dioxide and methane (CH4) fluxes were measured in a cutover bog of the Jura Mountains (France) together with biotic and abiotic variables for two entire vegetation periods in order to compare the carbon balance of the bog at three stages of regeneration. Among all factors, air temperature and vegetation index (including leaf area of vascular plants, bryophyte density and bryophyte desiccation) were the two main determinants of ecosystem respiration and gross photosynthesis at light saturation. During 2004 and 2005, the vegetated plots acted as carbon sinks. Net carbon exchange ranged between 67 and 166 g C m(-2) yr(-1) for the Eriophorum-dominated plots and between 93 and 183 g C m(-2) yr(-1) for the Sphagnum-dominated plots. The bare peat plots represented a net carbon source (between -19 and -32 g C m(-2) yr(-1)). Methane fluxes accounted for a very small part of the total carbon efflux (< 2%). The recovery of vegetation in our naturally regenerating bog was beneficial for the carbon sequestration after the relatively short period of 20 yr.