Tropical forest clearing threatens the sustainability of critically important global ecosystems services, including climate regulation and biodiversity. Indonesia is home to the world's third largest tropical forest and second highest rate of deforestation; as such, it plays an important role in both increasing greenhouse gas emissions and loss of biodiversity. In this study, a method is implemented for quantifying Indonesian primary forest loss by landform, including wetlands. A hybrid approach is performed for quantifying the extent and change of primary forest as intact and degraded types using a per-pixel supervised classification mapping followed by a GIS-based fragmentation analysis. The method was prototyped in Sumatra, and later employed for the entirety of Indonesia, and can be replicated across the tropics in support of REDD+ (Reducing Emissions from Deforestation and forest Degradation) initiatives. Mapping of Indonesia's wetlands was performed using cloud-free Landsat image mosaics, ALOS-PALSAR imagery and topographic indices derived from the SRTM. Results quantify an increasing rate of primary forest loss over Indonesia from 2000 to 2012. Of the 15.79 Mha of gross forest cover loss for Indonesia reported by Hansen et al. (2013) over this period, 38% or 6.02 Mha occurred within primary intact or degraded forests, and increased on average by 47,600 ha per year. By 2012, primary forest loss in Indonesia was estimated to be higher than Brazil (0.84 Mha to 0.47 Mha). Almost all clearing of primary forests (>90%) occurred within degraded types, meaning logging preceded conversion processes. Proportional loss of primary forests in wetlands increased with more intensive clearing of wetland forests in Sumatra compared to Kalimantan or Papua, reflecting a near-exhaustion of easily accessible lowland forests in Sumatra. Kalimantan had a more balanced ratio of wetland and lowland primary forest loss, indicating a less advanced state of natural forest transition. Papua was found to have a more nascent stage of forest exploitation with much of the clearing related to logging activities, largely road construction. Loss within official forest-land uses that restrict or prohibit clearing totaled 40% of all loss within national forest-land, another indication of a dwindling resource. Methods demonstrated in this study depict national scale primary forest change in Indonesia, a theme that until this study has not been quantified at high spatial (30m) and temporal (annual) resolutions. The increasing loss of Indonesian primary forests found in this study has significant implications for climate change mitigation and biodiversity conservation efforts
