The agriculture, forestry, and other land-use sector is a crucial sector, second only to the energy sector, in fighting climate change, and provides an important greenhouse gas abatement opportunity for the world. Recently, released figures for Australia, for example, suggest that agriculture, forestry, and other land-uses, which depend on healthy functioning ecosystems, could abate as much as three quarters of the country's emissions. The United Nations Framework Convention on Climate Change was concerned primarily with ecosystems and humankind, but the Kyoto Protocol of the Convention forfeited the potential of using agriculture, forestry, and other land-uses for global climate mitigation. This had the effect of decoupling biodiversity and ecosystems from carbon pollution reduction and climate change considerations. The Australian Carbon Pollution Reduction Scheme, one of the first emission trading schemes in the world to follow Kyoto “rules,” excludes the agriculture, forestry, and other land-use sector, apart from plantation reforestation, potentially creating perverse incentives that themselves can turn into threatening ecological processes. We use Australia and its emerging emissions trading scheme as a case study of the potential effects of this decoupling, and demonstrate the potential impacts on a landscape-scale regional greenhouse gas abatement and carbon sequestration project.