We present a fungal phylogeny based on mitochondrial NAD5 (subunit of the NADH dehydrogenase) protein sequences. The tree topology is well supported by bootstrap analysis and mostly congruent with trees inferred from nuclear sequences, ultrastructural data or mitochondrial COX1 and COX3 (subunits of the cytochrome oxidase) protein sequences. The NAD5 tree points to an early divergence of the Chytridiomycetes, an appearance of Zygomycetes prior to the divergence of Ascomycetes and Basidiomycetes, and Oomycetes as clearly unrelated to fungi. In addition, this analysis predicts a common ancestor of fungi and animals, to the exclusion of green algae and plants. Our results reinforce the view that protein sequences are of high value in the reconstruction of the phylogenetic history of mitochondria.