Phyllanthaceae are one of five segregates of Euphorbiaceae sensu lato recognised at family level by the Angiosperm Phylogeny group. The family contains c.2000 species in 59 genera. A new classification is done for this family based on the molecular studies using DNA sequence data of nuclear PHYC and plastid atpB, matK, ndhF and rbcL in conjuction with morphological characters. One of the major contribution from our molecular phylogeny is the division of the family into two strongly supported clades which represents the two subfamilies Antidesmatoideae and Phyllanthoideae and ten tribes. Further, Phylogenetic relationships within tribe Phyllantheae, the largest tribe of the family Phyllanthaceae, were examined with special emphasis on Phyllanthus which is one of the economically important genus. ITS nuclear ribosomal and plastid matK DNA sequence data for roughly 100 species of tribe Phyllantheae were analyzed including representatives of all published subgenera of Phyllanthus .We recognize six lineages at generic rank in tribe Phyllantheae: Flueggea s.l., Lingelsheimia, Margaritaria, Phyllanthus s.l., Plagiocladus, and Savia section Heterosavia. Richeriella should be united with Flueggea, and the generic status of Plagiocladus (= Phyllanthus diandrus) is confirmed. Results confirm paraphyly of Phyllanthus having Breynia, Glochidion, Reverchonia, and Sauropus embedded within. Phyllanthus maderaspatensis is sister to all other species of Phyllanthus s.l., and the genus appears to be of Old World origin. The unique branching architecture, "phyllanthoid branching", of most Phyllanthus taxa has been lost (and/or has evolved) repeatedly. Taxonomic divisions based on similar pollen morphology are largely confirmed, and related taxa share similar distributions. Ancestral areas were reconstructed from one of the most parsimonious tree, using MP analysis from the combined data with the DIVA program, version 1.1 Current distribution areas for the genera of Phyllanthaceae were coded in eight categories (Asia, Africa, Australia, Madagascar, Mediterranean, North America, South America, and West Indies). The relative timing shows that this family originated from Africa, but further work on divergence time using fossil record from a related family (Clusiaceae) is in progress and this will be published soon.