Previous estimates of phylogeny in the Phyllanthaceae, Phyllantheae, have been hampered by undersampling of species from morphologically distinctive groups and using too few gene regions. To increase the phylogenetic resolution, sequences of two nuclear (ITS1–5.8S–ITS2) and Phytochrome C (PHYC)) and two non-coding chloroplast (accD–psaI, trnS–trnG) DNA markers were analysed using maximum parsimony and Bayesian inference with expanded sampling in Breynia, Glochidion, Sauropus and Synostemon. Our results supported reinstatement of Synostemon, previously included in Sauropus s.str., to generic rank, and provided evidence towards its future infrageneric classification. The results also indicated expansion of Breynia to include Sauropus s.str.; this combined monophyletic group consists of two strongly supported clades. Finally, we showed monophyly for Glochidion, which is sister to Phyllanthus subg. Phyllanthodendron, both still remaining undersampled. Morphological features characteristic of Breynia, Sauropus and Synostemon are discussed, as well as the desirability of dividing Phyllanthus into smaller genera.