The phylogenetic relationship of 52 specimens representing 30 species of Anthracoidea (Ustilaginales) was investigated by molecular analyses using sequence data from the large subunit (LSU) of nuclear rDNA. Phylogenetic trees were inferred with neighbour-joining (NJ), maximum parsimony (MP), and Bayesian Markov chain Monte Carlo (MCMC) methods. The results are discussed with respect to the species concept and the subdivision of the genus into subgenera and sections. Collections from different hosts and localities were compared. Our analyses can neither support nor significantly reject the hypothesis of the bipartition of the genus Anthracoidea. Thus, the representatives of the subgenus Proceres appeared in the NJ analysis as a moderately supported monophylum, whereas MCMC analysis revealed a polyphyletic topology for this group. Paraphyly of the subgenus Anthracoidea was supported by all methods used. Sections Echinosporae and Leiosporae were each represented by two species in our analyses which grouped together with high support. Section Anthracoidea should be restricted to a highly supported group with extremely irregular to angular teliospore shape. However, these three sections do not cover the whole diversity of the subgenus Anthracoidea. Molecular data largely supported the traditional circumscription of species, and species delimitations are discussed.