The phylogenetic relationships of several smut fungi parasitic on dicotyledons were analysed. Parsimony analysis was performed based on the sequences of the ITS regions of the rDNA genes. Three genera were considered: Microbotryum, Sphacelotheca and Ustilago. The cladogram showed a dichotomy: the species of Microbotryum and Ustilago parasitic on dicotyledons (dicot Ustilago) were found to be divided into two independent taxa among the Microbotryaceae. A divergent mechanism of evolution of the species of each of these two clades with their respective hosts could be involved in this dichotomy. According to our results, Microbotryum appears monophyletic and restricted to the anthericolous smuts on Caryophyllaceae. However, no morphological characters have yet been found to support this distinction, and we refute the denomination Bauhinus as defined by Moore to describe the group of ‘dicot Ustilago’ as it leads to controversial determinations. Sphacelotheca belongs to Microbotryales, but could not be synonymised with Microbotryum as S. polygoni-persicariae is in an independent clade. Lastly, U. duriaeana is independent of the ‘dicot Ustilago’ clade; the position of this species among Microbotryales is still uncertain.