The subclass Microbotryomycetidae (Basidiomycota, Urediniomycetes) comprises a remarkably diverse assemblage of fungi. This group includes phytoparasites, mycoparasites and probably also saprobes that show a wide range of ecological preferences. In order to study the phylogenetic relationships within the Microbotryomycetidae, and to develop a more natural classification system, mitosporic and meiosporic taxa were investigated using an integrated approach. Sequence data of 26S rDNA D1/D2 domains were analyzed using several procedures, including the Bayesian Markov chain Monte Carlo method of phylogenetic inference. Ultrastructural markers such as the type of septal pore and presence / absence of colacosomes were investigated and micromorphological and nutritional properties were compared. In this study the current concept of the genus Leucosporidium and its apparent polyphyletic nature were addressed, as well as the relationships of this genus with the Microbotryales and Mastigobasidium. The classification of the anamorphic species closely related to Leucosporidium, and the concepts of the order Sporidiales and family Sporidiobolaceae were also reviewed.