Insular Southeast Asia experienced the highest level of deforestation among all humid tropical regions of the world during the 1990s. Owing to the exceptionally high biodiversity in Southeast Asian forest ecosystems and the immense amount of carbon stored in forested peatlands, deforestation in this region has the potential to cause serious global consequences. In this study, we analysed deforestation rates in insular Southeast Asia between 2000 and 2010 utilizing a pair of 250 m spatial resolution land cover maps produced with regional methodology and classification scheme. The results revealed an overall 1.0% yearly decline in forest cover in insular Southeast Asia (including the Indonesian part of New Guinea) with main change trajectories to plantations and secondary vegetation. Throughout the region, peat swamp forests experienced clearly the highest deforestation rates at an average annual rate of 2.2%, while lowland evergreen forests declined by 1.2%/yr. In addition, the analysis showed remarkable spatial variation in deforestation levels within the region and exposed two extreme concentration areas with over 5.0% annual forest loss: the eastern lowlands of Sumatra and the peatlands of Sarawak, Borneo. Both of these areas lost around half of their year 2000 peat swamp forest cover by 2010. As a whole this study has shown that deforestation has continued to take place on high level in insular Southeast Asia since the turn of the millennium. These on-going changes not only endanger the existence of numerous forest species endemic to this region, but they further increase the elevated carbon emissions from deforested peatlands of insular Southeast Asia thereby directly contributing to the rising carbon dioxide concentration in the atmosphere.