The present study aimed to analyze and compare the chemical profile and antioxidant capacity of propolis from different bee species and different regions. The chemical profiles of propolis from six stingless bee species (Tetragonula iridipennis, T. laeviceps, Lepidotrigona terminata, L. ventralis, Lisotrigona carpenteri and Homotrigona apicalis) collected from a total of eight locations in Vietnam were investigated by gas chromatography–mass spectrometry (GC-MS). More than 70 compounds were identified, amongst which phenolic lipids (cardanols, resorcinols and anacardic acids), aromatic acids, triterpenes and xanthones. Taxonomic markers for Mangifera indica (phenolic lipids and cycloartane triterpenes) were detected in propolis from bees of the genera Tetragonula and Lepidotrigona, although in different amounts, whereas propolis from H. apicalis was characterized by triterpenes of the amyrine type, typical of dipterocarp trees. A clear discrimination between both groups was observed by principal component analysis (PCA) and partial least squares–discriminant analysis (PLS-DA). Propolis from Tetragonula and Lepidotrigona spp. and from Lisotrigona carpenteri, which is rich in xanthones, possesses higher radical scavenging and ferric-reducing capacity than that from H. apicalis. Propolis produced by all six stingless bee species in Vietnam was analyzed for the first time. In addition, this is the first report on L. carpenteri propolis.