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Coastal mangrove forests provide a broad array of ecosystem services including fisheries production, sediment regulation, wood production and protection from storms and tsunamis. Similarly, peat swamp forests harbour a diverse range of flora and fauna, regulate water regimes and store large amounts of carbon deposited in organic materials below the ground. In Southeast Asia, the conversion rates of mangrove to other land uses, such as shrimp farms and settlements, are among the highest for any forest type. Furthermore, the conversion of peat swamp forests to oil palm and pulp wood plantations and the associated fires have been the main sources of greenhouse gas (GHG) emissions in the region during the past decade. With deforestation accounting for around 17% of global anthropogenic GHG emissions, the upcoming global mechanism known as Reducing Emissions from Deforestation and forest Degradation (REDD+) provides an important climate change mitigation option. This scheme offers economic incentives for conserving forests and associated carbon (C) stores in developing countries. Mangrove and peat swamp ecosystems are well suited to such strategies. However, although their high rates of C assimilation and export (fluxes) are known, their total C storage—the amount that may be emitted upon conversion—has not been well quantified. We measured total ecosystem C storage (above and below ground) in mangrove ecosystems in North Sulawesi, Central Kalimantan and Central Java, Indonesia. We assessed variations in mangrove C-pools along transects running inland from the ocean edge, as well as their vulnerability to sea-level rise and land use. In addition, in Tanjung Puting National Park, Central Kalimantan, we sampled both the total aboveground biomass and the belowground peat horizons to ascertain total ecosystem C-pools. Summary Our measurements show that total carbon storage in mangrove ecosystems is exceptionally high compared with most forest types, with a mean of 968 Mg C ha –1 and range of 863–1073 Mg C ha –1 . These carbon stocks result from a combination of large-stature forest (trees up to ~2 m in diameter) and organic-rich peat soils to a depth of 5 m or more. Aboveground C-stocks vary widely depending on stand composition and history, but belowground pools comprise a large portion of ecosystem C storage in most sites. Although mangrove composition is often stratified with distance from the ocean edge, C storage does not vary consistently along this gradient. Ecosystem C-pools at Tanjung Puting exceed 1000 Mg ha –1 in many of the sampled locations. All sampled stands had a depth to mineral soil of less than 1 m, with a mean peat depth of 45.5 ± 6.8 cm. Mean total C-stock was 894.3 Mg C ha –1 , with a range of 558– 1213 Mg C ha –1 . It should be noted, when considering these estimates of ecosystem pools, that peat depths of tropical peat swamp forests may be as much as 20 m (with an average depth of 3–5 m). Projected rates of sea-level rise (~1 cm yr –1 over the next century) are ~5–10 times higher than typical mangrove sediment accrual rates (1–2 mm yr –1 ), suggesting high susceptibility and a potential positive feedback via loss of C-stocks. Thus, the combination of very high C-stocks, susceptibility to land use activities and numerous ecosystem services makes tropical mangroves ideal candidates for REDD+, particularly if climate change mechanisms can be applied to promoting synergies between adaptation to climate change (e.g. local migration) and mitigation. However, additional studies to better quantify ecosystem C-pools and the potential impact of land cover change and fire are greatly needed in order to make sound policy decisions related to carbon financing through the REDD+ mechanism