The classification of Phellinus s.l., Inonotus s.l. and the phylogenetic relationships of allied genera were studied using nuc-lsu rDNA sequence data. The worldwide taxon sampling comprised 107 species, 99 of them belonging to the Hymenochaetales. The phylogenetic trees were discussed in relation to morphological and anatomical features of the fruit bodies. The Hymenochaetales formed no monophyletic group and several non-Hymenochaetales appeared as intermingled with the Hymenochaetales. Trichaptum abietinum and Oxyporus populinus showed no certain affinities within the Hymenochaetales, whereas Basidioradulum radula was closely related to Phellopilus nigrolimitatus, and Hyphodontia quercina and Schizopora paradoxa were related to Coltricia, Coltriciella and Pyrrhoderma adamantinum. Phellinus s.l. and Inonotus s.l. formed no monophyletic groups, and a subdivision in the following genera is accepted: Phellinus s.s., Inonotus s.s., Inocutis, Fomitiporella, Aurificaria, Phylloporia, Fulvifomes, Mensularia, Pseudoinonotus, Fomitiporia, Porodaedalea, Onnia, Fuscoporia, and Inonotopsis. Coltricia and Coltriciella were confirmed as seperate genera. The taxonomic status of Phellinidium and Pyrrhoderma remained uncertain. 16 new combinations are proposed.