In the second part of the taxonomic revision of Phyllanthus L. in Madagascar and the Comoro Islands the subgenera Anisonemoides (Jean F. Brunel) Ralim. & Petra Hoffm., stat. nov. and Menarda (Müll. Arg.) Ralim. & Petra Hoffm., stat. nov. are described. The subgenera are characterised by pinnatiform or bipinnatiform phyllanthoid branching, stamens are (2-4)5(-6) free or fused in Anesonemoides but 5, free stamens in Menarda; dehiscent fruits and tricolporate or trisyncolporate pollen with a macro-microreticulate exine, with muri bordering colpi, and one or two pores. They are endemic to Madagascar with most taxa being of limited geographic distribution. The subgenus Anisonemoides, stat. nov. comprises fifteen species and two species are belonging to Menarda, stat. nov. Four species from the Eastern floristic domain are newly described: Phyllanthus bemangidiensis Ralim., sp. nov., P. coodei Ralim. & Petra Hoffm., sp. nov., P. gordonii Ralim. & Petra Hoffm., sp. nov., and P. mantadiensis Ralim. & Petra Hoffm., sp. nov. Distribution maps and IUCN conservation assessment status are provided for each taxon. The circumscription of several species within Anisonemoides stat. nov. and Menarda stat. nov. has been revised.