Abstract Aim To reconstruct the palaeoenvironments of megafauna-bearing sites from Pleistocene Southeast Asia, and to describe general environmental changes in the region. Location Indochina and Sundaland, including Myanmar, Laos, Vietnam, Cambodia, Thailand, the Malay Peninsula, Borneo, Sumatra and Java. Methods This study reconstructs the habitat types of 25 Pleistocene sites in Southeast Asia through a synecological (community-based) method. This method specifically targets medium- and large-bodied mammals, and ecovariables that could be directly assessed from species lists were chosen. The methods allow the reconstruction of fossil sites as closed (continuous tree cover), mixed (heterogeneous tree cover) and open (very limited to no tree cover) through discriminant functions analysis of community guild structure. Results Four Pleistocene sites can confidently be assigned to one of the three habitat types. Tam Hang (south), a Middle Pleistocene site from Laos, is classified as mixed. Ban Fa Suai, a Middle Pleistocene site from Thailand, is also classified as mixed. Trinil, a Middle Pleistocene site from Java, is classified as open. Lastly, Hang Hum II, a Late Pleistocene site from Vietnam, is classified as open. Insufficient species are present in the fossil faunas of remaining sites to allow statistically confident habitat assignment. Nevertheless, conditional habitat assignments can be achieved, and these are largely congruent with other palaeoenvironmental evidence. Main conclusions Medium- and large-bodied mammals are the most frequently recovered mammals from Pleistocene sites in Southeast Asia. Previous palaeoenvironmental reconstructions of these sites have been hampered by this body size bias, as well as by limited site and faunal descriptions. However, our analysis demonstrates that reconstructions can still be achieved for megafauna-bearing sites in the region. The reconstructions suggest that through much of the Pleistocene, Southeast Asia had significant areas of mixed habitats, and that the widespread distribution of rain forests, such as found today, was a relatively rare phenomenon.