Species belonging to Hypoxylon and related genera are bark pathogens and wood decay agents of angiosperms, sometimes able to live asymptomatically in host tissues. In the present work the ITS regions of the ribosomal DNA from 21 isolates belonging to five species were sequenced and then compared with each other. A phylogenetic parsimony analysis among isolates was carried out. ITS2 appears to be the most informative among the sequenced portions of rDNA. Results are strictly consistent with the latest taxonomic arrangements obtained with classical morphological approaches. The ITS sequence analysis is an efficient and accurate method for discriminating among taxa of Hypoxylon and related genera.