Ribosomal DNA sequences of the 28S large subunit gene have suggested a close relationship between the poroid mushroom genus Polyporus s. str., segregate genus Pseudofavolus, and non-poroid Mycobonia occurring in the Americas. We re-investigated this phylogeny using the variable ITS spacers of ribosomal DNA and predicted partial transcript structure. Partial secondary structures of pre-processed RNA molecules (ITS2 rRNA), predicted from nine sequences, are described as taxonomic characters indicative of the Polyporus - Pseudofavolus - Mycobonia alliance. We therefore emend Polyporus to include Mycobonia.