The genus Phyllanthus is paraphyletic as currently circumscribed, with the genera Breynia, Glochidion and Synostemon nested within it. A phylogeny based on nuclear (ITS, PHYC) and chloroplast (matK, accD-psaI, trnS-trnG) markers is presented, including 18/18 subgenera and 53/70 sections. Differences in habit, branching type, floral and fruit characters are discussed, and we find indications for shifts in pollination and dispersal strategies possibly underlying the convergent evolution of these characters in multiple clades. Several taxonomic issues were found in the subgeneric classification of Phyllanthus that will require new transfers and rank changes. Phyllanthus subg. Anesonemoides, subg. Conami, subg. Emblica, subg. Gomphidium, subg. Kirganelia and subg. Phyllanthus are polyphyletic, and several sections appear to be paraphyletic (e.g., P. sect. Anisonema, sect. Emblicastrum, sect. Pseudoactephila, sect. Swartziani, and sect. Xylophylla); P. subg. Phyllanthodendron is furthermore paraphyletic with the genus Glochidion nested within. To create a classification of tribe Phyllantheae that comprises exclusively monophyletic taxa, it is necessary to treat several clades at the same taxonomic rank as the genera Breynia, Glochidion and Synostemon. Since combining all genera would lead to one giant heterogeneous genus that is difficult to define, we recommend dividing Phyllanthus into several monophyletic genera, which have previously been recognized and often possess diagnostic (combinations of) morphological characters. This new classification is forthcoming.