Superoxide dismutases (SODs), which provide protection against oxidative stress, exhibit an essential role for fungal cell survival, especially during host invasion. Here, 20 partial SOD sequences from 19 pathogenic fungi were determined and aligned with 43 homologous fungal sequences from databases. All sequences encoded tetrameric manganese (Mn)-containing SODs showing predicted cytosolic or mitochondrial subcellular localization. Numerous fungi possessed both cytosolic and mitochondrial MnSODs in addition to the mainly cytosolic copper/zinc isozyme. Moreover, MnSOD sequence variability was higher than SSU rRNA and similar to ITS rRNA, suggesting MnSOD could be used to identify closely related fungal species. MnSOD- and SSU rRNA-based phylogenetic trees were constructed and compared. Despite a more complex topology of the MnSOD tree, due to several gene duplication events, all the classic fungal classes and orders were recovered. A salient point was the existence of two paralogous cytosolic and mitochondrial MnSODs in some Ascomycota. A hypothetical evolutionary scenario with an early gene duplication of the "mitochondrial" gene is proposed.