Identifying hotspots of greenhouse gas (GHG) emissions from terrestrial ecosystems on global and regional scales is pivotal to limiting the future increase of GHG concentrations in the atmosphere, and to assisting in the targeting of effective mitigation strategies. Hotspot identification, however, needs to be based on a multi-dimensional approach that considers realistic biophysical, agronomic, economic and social constraints. This special issue is open to contributions that relate to the general topic of terrestrial GHG hotspots, including but not restricted to improved GHG data sets that solve current data gaps, ii) improved estimations of GHG data uncertainties, iii) improved interoperability of databases on different scales (spatio–temporal) and streams (i.e. satellite remote sensing, ground measurements), iv) inclusion of socio-economic dimensions in GHG mitigation strategies, and vi) considerations of mitigation strategies. This analysis is supported by the CGIAR research programmes on Climate Change, Agriculture and Food Security (CCAFS) and Forests, Trees and Agroforestry (FTA), which have a focus on mitigation interventions from smallholder systems in the developing world.