Peniophora is an old corticioid genus, from which two small satellite genera, Dendrophora and Duportella, were derived based on morphological differences. Molecular systematic studies showed that they belong to Peniophoraceae, Russulales, but the inter- and intra-generic phylogenetic relationships are still unclear. Moreover, the species diversity of this group in subtropical and tropical Asia has not been sufficiently investigated and studied. In this study, we carried out an intensive taxonomic and phylogenetic study on Peniophora sensu lato based on analyses of concatenated ITS1-5.8S-ITS2 (ITS, Internal Transcribed Spacer) and 28S (D1–D2 domains of nuc 28S rDNA) sequence data of all available species worldwide. In the phylogenetic trees, species of Peniophora s. l. (sensu lato) including types of Peniophora s.s. (sensu stricto), Dendrophora and Duportella were interspersed within a strongly supported clade. It means that the morphological delimitations of the three genera are not reliable, and they should be regarded as a large genus. As a result, eight species of Duportella were transferred to Peniophora, although five of them have not been sequenced. Four new distinct lineages, corresponding to Peniophora cremicolor, P. major, P. shenghuae and P. vietnamensis spp. nov., were recovered in the trees. Peniophora taiwanensis is treated as a later synonym of P. malaiensis based on morphological and molecular evidence. Duportella renispora is excluded from Peniophoraceae, because BLAST results of the ITS and 28S sequences of the holotype showed that it is closely related to Amylostereum. Descriptions and illustrations are provided for the four new species, and an identification key is given for all 25 species of Peniophora in China. Our results indicated that the species diversity of the corticioid fungi in Asia is rich and deserves further study.