This policy brief discusses the nature of climate change mitigation and adaptation in the wetland ecosystems of Indonesia. It describes the ecosystem services which accrue from peatland and mangrove forests and outlines the research themes of an international workshop held in Bali during April 2011. The brief makes the following recommendations: 1) the roles of tropical wetlands are currently understated in IPCC Guidelines and the scientific community should aim to overcome knowledge gaps to rectify this issue; 2) carbon-rich tropical wetlands must be understood as high priorities in climate change adaptation and mitigation strategies; 3) a multi-disciplinary scientific approach is needed to assist Indonesia in protecting it’s tropical wetlands; 4) a research agenda must be well co-ordinated to ensure that it remains relevant to the policy community; 5) research organizations should co-ordinate and collaborate to minimise overlaps.