The landscapes in the discontinuous permafrost area of Western Siberia are unique objects for assessing the direct and indirect impact of permafrost on greenhouse gas fluxes. The aim of this study was to identify the influence of permafrost on the CO2 emission at the landscape and local levels. The CO2 emission from the soil surface with the removed vegetation cover was measured by the closed chamber method, with simultaneous measurements of topsoil temperature and moisture and thawing depth in forest, palsa, and bog ecosystems in August 2022. The CO2 emissions from the soils of the forest ecosystems averaged 485 mg CO2 m−2 h−1 and was 3–3.5 times higher than those from the peat soils of the palsa mound and adjacent bog (on average, 150 mg CO2 m−2 h−1). The high CO2 emission in the forest was due to the mild soil temperature regime, high root biomass, and good water–air permeability of soils in the absence of permafrost. A considerable warming of bog soils, and the redistribution of CO2 between the elevated palsa and the bog depression with water flows above the permafrost table, equalized the values of CO2 emissions from the palsa and bog soils. Soil moisture was a significant factor of the spatial variability in the CO2 emission at all levels. The temperature affected the CO2 emission only at the sites with a shallow thawing depth.