Phylogenetic and molecular clock analyses were performed including all genera except one (Pseudomonotes) for the three subfamilies of Dipterocarpaceae. We also included representatives of Sarcolaenaceae and Cistaceae with Bixaceae as the ultimate outgroup. Three plastid regions (six markers), partial rbcL, trnK-matK-trnK (partial trnK intron including complete matK) and trnT-trnL-trnF (partial trnT, complete trnT-trnL intergenic spacer, complete trnL, complete trnL-trnF intergenic spacer and partial trnF), were analysed. We also investigated additional accessions for genome size and chromosome numbers. Our phylogenetic results differ in three important respects from previous interpretations of morphological characters, as reflected in recent classifications. First, our analyses strongly support assignment of Pakaraimaea (subfamily Pakaraimaeoideae) to Cistaceae. Second, the morphological concepts of Dipterocarpeae and Shoreeae in subfamily Dipterocarpoideae are not supported because Dipterocarpus is sister to Dryobalanops plus tribe Shoreeae. Our analysis revealed four clades: (1) Dipterocarpus; (2) Dryobalanops, for which tribal assignment has been contentious; (3) genera of Shoreeae; and (4) the remaining genera of Dipterocarpeae. Third, Shorea is not monophyletic. Monotoideae are weakly supported as sister to Dipterocarpoideae; Sarcolaenaceae (endemic to Madagascar) are sister to this pair. Divergence in extant Dipterocarpoideae occurred c. 55 Mya. Genome sizes for all accessions examined are small (0.3264-0.6724 pg), and the additional chromosome numbers we collected fit into the patterns previously observed for Dipterocarpaceae.