Global warming expects shifting natural zones northward and stimulating a degradation of the permafrost (IPCC, 2001). As a consequence, the acceleration of the soil organic matter decay in soils and the increase of biomass production in vegetation are proposed. The net balance of these two processes is thought to be transforming the high latitudes ecosystems into a source of CO2, which in turn contributes to the increase of the gas concentration in the atmosphere. This theory is built on general assumptions on few of the episodic and spatially seldom field samplings, and has to be empirically approved. The objectives of the study are: (1) to understand mechanisms and drivers of carbon cycle in different bio-climatic zones and permafrost-affected regions; (2) to analyze the changes in carbon cycle due to possible replacement of the zones and shrinking of permafrost. The study is built on recent inventory of carbon pools and fluxes associated with digitized maps of the major ecosystems components (soil, vegetation, riverin discharge) integrated by means of GIS (Stolbovoi and McCallum, 2002). Russia comprises a range of frost-affected regions from which 560*106 ha (35% of the country) are seasonally frozen, 223*106 ha (14% of the country) have a sporadic permafrost, 227*106 ha (14% of the country) covered by discontinuous permafrost and, 581*106 ha (36% of the country) have continuous permafrost (Stolbovoi, 2005). The biomass density is considerably less in the regions with continuous permafrost in all natural zones. Net primary production does not show much difference between regions in the tundra zone and it declines in the permafrost-affected regions in middle taiga zone. Carbon density in soils is generally higher in topsoil and total soil in forest, grassland and shrubs for permafrost-affected regions. Aggregated indicators of C cycle show rather mosaic picture, e.g., net ecosystem production (NEP) is higher for forests in permafrost-affected regions than in the seasonally frozen. The pattern of net biome production (NBP) follows the NEP but is slightly smoothed my forest disturbances (wild fires) that are common for remote permafrost regions. NEP and NBP for grasses and shrubs shows reverse picture and are less in permafrost-affected regions. Ecosystem carbon balance (ECB) is negative for forests that are seasonally frozen and is positive in permafrost-affected regions. For all regions, the ECB is negative for deep peat and is positive for shallow peat. The study illustrates that various frost-affected regions are highly varied by soils. The forecasted alteration of the C pools, as a “black-box” reaction on the climate warming is oversimplified and confusing. In reality, this alteration may be seen through the analysis of soil development. The trajectories of the latter are soil specific and driven by complicated evolution of different soil forming factors. The study reveals that permafrost-affected regions are the sink and seasonally frozen regions are the source for CO2 in Russia at present. This pattern remains to be the same under predicted rise in temperature unless the change in precipitation, hydrological regime and aridization will not be significant.