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The pilot project of the Ministry of Education and Science of the Russian Federation aims to collect new data on the emission and absorption of greenhouse gases (GHG) in natural ecosystems. Soils perform many ecological functions in terrestrial ecosystems. In particular, they serve as a source of CO2, a sink and a source of methane (CH4) to the atmosphere. Obtaining reliable data on GHG fluxes, including GHG emission and uptake by soils, is the basis for obtaining reliable data on the GHG balance in natural ecosystems of Russia. In this study, the spatial heterogeneity of CO2 and CH4 soil fluxes as well as their seasonal and diurnal variability were determined by field measurements of CO2 and CH4 fluxes using the chamber method at different experimental plots of carbon supersites in Krasnodar and Moscow regions. In addition, the dependence of CO2 and CH4 fluxes on soil temperature and moisture was determined. The flux measurements at the carbon supersite in the Krasnodar region were carried out on a coastal area of the Black Sea covered with heterogeneous herbaceous, shrub and forest vegetation. A portable soil Smart Chamber (LI-COR, USA) connected to an infrared gas analyzer LI-7810 (LI-COR, USA) was used for flux measurements. A HydraProbe sensor (Stevens, USA) was used to measure soil temperature and moisture. Measurements of CO2 fluxes at the carbon supersite in the Moscow Region were conducted on six experimental plots located in agrolandscapes and typical forest and grassland biogeocenoses of the southern European taiga. A portable chamber system connected to a portable analyzer LICA PS-9000 (LICA United Technology Limited, China) was used for flux measurements. The measurement results showed significant spatial and temporal variability of GHG fluxes determined by landscape features of the experimental sites, as well as by temperature and moisture of the upper soil layer. The measurements showed well manifested seasonal and diurnal variations, largely determined by temperature variability. All ecosystems served as a permanent source of CO2 to the atmosphere during the entire measurement period. At the same time, all experimental sites of the carbon supersite in the Krasnodar region served as a permanent CH4 sink from the atmosphere. The analysis of the dependence of CO2 and CH4 fluxes on soil temperature and moisture showed that the increase of soil temperature in different temperature intervals can lead to multidirectional trends in the change of CO2 emission and CH4 uptake by the soil. At soil temperatures below 28-30°C, an increase in CO2 emission from the soil surface was observed, whereas at higher temperatures (>30°C), soil CO2 emission tends to decrease with increasing temperature. An increase in soil water content leads to an increase in CO2 emission due to an increase in the activity of soil microorganisms and root respiration. The dependence of CH4 flux on temperature and soil moisture was manifested by an increase in soil CH4 uptake with decreasing soil moisture and increasing temperature. Field studies at the carbon supersite in the Moscow region were supported by the Most Important Innovative Project of National Importance of Russia, MIIP NI (registration number 123030300031-6) and the MSU Development Program (project 23-SCH07-55). Studies at the carbon supersite in Krasnodar region were supported by the State Assignment of the Shirshov Institute of Oceanology of the Russian Academy of Sciences (FMWE-2023-0001).