Besides water vapour, greenhouse gases CO₂, CH₄, O₃ and N₂O contribute ~60%, 20%, 10% and 6% to global warming, respectively; minor contribution is made by chlorofluorocarbons and volatile organic compounds (VOC). We present CO₂, CH₄ and N₂O fluxes from natural and relatively unmanaged soil–plant ecosystems (the ecosystems minimally disturbed by direct human or human-induced activities). All natural ecosystems are net sinks for CO₂, although tundra and wetlands (including peatlands) are large sources of CH₄, whereas significant N₂O emissions occur mainly from tropical and temperate forests. Most natural ecosystems decrease net global warming potential (GWP) from –0.03 ± 0.35 t CO₂-e ha^–1 y^–1 (tropical forests) to –0.90 ± 0.42 t CO₂-e ha^–1 y^–1 (temperate forests) and –1.18 ± 0.44 t CO₂-e ha^–1 y^–1 (boreal forests), mostly as CO₂ sinks in phytobiomass, microbial biomass and soil C. But net GWP contributions from wetlands are very large, which is primarily due to CH₄ emissions. Although the tropical forest system provides a large carbon sink, the negligible capacity of tropical forests to reduce GWP is entirely due to N₂O emissions, possibly from rapid N mineralisation under favourable temperature and moisture conditions. It is estimated that the natural ecosystems reduce the net atmospheric greenhouse gas (GHG) emissions by 3.55 ± 0.44 Gt CO₂-e y^–1 or ~0.5 ppm_v CO₂-e y^–1, hence, the significant role of natural and relatively unmanaged ecosystems in slowing global warming and climate change. However, the impact of increasing N deposition on natural ecosystems is poorly understood, and further understanding is required regarding the use of drainage as a management tool, to reduce CH₄ emissions from wetlands and to increase GHG sink from the restoration of degraded lands, including saline and sodic soils. Data on GHG fluxes from natural and relatively unmanaged ecosystems are further compounded by large spatial and temporal heterogeneity, limited sensitivity of current instruments, few and poor global distribution of monitoring sites and limited capacity of models that could integrate GHG fluxes across ecosystems, atmosphere and oceans and include feedbacks from biophysical variables governing these fluxes.