Inter-annual and seasonal variations of energy, vapor water, and carbon fluxes and associated climate variables in a middle taiga pine (Pinus sylvestris) forest on sandy soils and in a northern taiga larch (Larix gmelinii) forest on permafrost in central Siberia were studied from eddy covariance measurements acquired during the growing seasons of 1998–2000 and 2004–2008, respectively. Both the pure Scots pine of 215-year-old and pure Gmelin larch of 105-year-old forests naturally regenerated after forest fires, differed by their tree stand characteristics, and grew in extremely contrasting environments with distinctive climatic and soil conditions. Net radiation was greater in the pine forest due to higher values in the summer months and a longer growing season. Sensible heat flux was the larger term in the radiation balance in both forests. The Bowen ratio stayed between 1 and 2 during the growing season and was as high as 8–10 in dry spring in both forests. In the dry summers, latent heat explained 70%–80% of the daily net ecosystem CO2 exchange (NEE) variation in both forests. The average NEE was significantly smaller in the larch ecosystem at −4 µmol m−2s−1 compared to −7 µmol m−2s−1 in the pine forest. NEP for the growing season was 83 in the larch forest on continuous permafrost and 228 g C m−2 in the pine forest on warm sandy soils. Water use efficiency was 5.8 mg CO2 g−1H2O in the larch forest and 11 mg CO2 g−1H2O in the pine forest and appeared to be consistent with that in boreal forests. As a result of the forest structure change from Gmelin larch to Scots pine due to the permafrost retreat in a warming climate, the boreal forest C-sink may be expected to increase. Thus, potential feedback to the climate system in these “hot spots” of forest-forming replacement species may promote C-uptake from the atmosphere. However, as many studies suggest, in the pace of transition from permafrost to non-permafrost, C-sink would turn into C-source in hot spots of permafrost retreat.