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Clear-cutting and other forest disturbances drive the energy, water vapor and greenhouse gas fluxes between boreal forest ecosystems and the atmosphere and can influence climate conditions at local to global scales. The effects of clear-cutting on the ecosystem-atmosphere fluxes substantially vary between different forest types and are closely dependent on local environmental conditions. In this study, we analyze the effects of clear-cutting on the energy and CO exchange using new results of eddy covariance flux measurements in undisturbed mature and clear-cut forest ecosystems during the two growing seasons following harvest. The results show increased albedo at the clear-cut site compared with undisturbed forest and lower values of net radiation, latent (LE) and sensible (H) heat fluxes. The mean seasonal Bowen ratio (β) was about 0.5 at both sites in the first year, and 0.2 at the mature forest site and about 0.3 at the clear-cut site in the second year. The harvested site was a CO source for the atmosphere during the entire period of measurements (net ecosystem exchange (NEE) = 3.3± 1.3 in 2016 and 1.2 ± 2.3 gC∙m ∙d in 2017), whereas the CO budget of the undisturbed forest was close to neutral (0.1 ± 2.1 gC∙m ∙d in 2016 and -0.1 ± 2.2 gC∙m ∙d in 2017). The total ecosystem respiration (TER) was very similar at both sites (7.3 ± 2.4 gC∙m ∙d in 2016 and 8.0 ± 2.9 gC∙m ∙d in 2017 at the clear-cut site, 7.9±3.1 gC∙m ∙d in 2016 and 8.5 ± 2.1 gC∙m ∙d in 2017 at the mature forest site). The gross primary production (GPP) after the harvesting demonstrated a fast recovery and tended towards the GPP of the undisturbed forest (4.7 ± 2.9 gC∙m ∙d in 2016 and 6.1 ± 3.1 gC∙m ∙d in 2017 at the clear-cut site, 7.8 ± 3.8 gC∙m ∙d in 2016 and 8.6 ± 4.6 gC∙m ∙d in 2017 at the mature forest site). The obtained NEE, GPP and TER values at the clear-cut site of the southern taiga are relatively high compared with boreal clear-cut sites where carbon dioxide fluxes have been previously reported. This study was supported by a grant from the Russian Science Foundation (14-14-00956)