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Background  Species of the  Fusarium  genus are important fungi which is associated with health hazards in human and animals. The taxonomy of this genus has been a subject of controversy for many years. Although many researchers have applied molecular phylogenetic analysis to examine the taxonomy of  Fusarium  species, their phylogenetic relationships remain unclear only few comprehensive phylogenetic analyses of the  Fusarium  genus and a lack of suitable nucleotides and amino acid substitution rates. A previous stugy with whole genome comparison among  Fusairum  species revealed the possibility that each gene in  Fusarium  genomes has a unique evolutionary history, and such gene may bring difficulty to the reconstruction of phylogenetic tree of  Fusarium . There is a need not only to check substitution rates of genes but also to perform the exact evaluation of each gene-evolution.    Results  We performed phylogenetic analyses based on the nucleotide sequences of the rDNA cluster region (rDNA cluster), and the β-tubulin gene ( β-tub ), the elongation factor 1α gene ( EF-1α ), and the aminoadipate reductase gene ( lys2 ). Although incongruence of the tree topologies between  lys2  and the other genes was detected, all genes supported the classification of  Fusarium  species into 7 major clades, I to VII. To obtain a reliable phylogeny for  Fusarium  species, we excluded the  lys2  sequences from our dataset, and re-constructed a maximum likelihood (ML) tree based on the combined data of the rDNA cluster,  β-tub , and  EF-1α . Our ML tree indicated some interesting relationships in the higher and lower taxa of  Fusarium  species and related genera. Moreover, we observed a novel evolutionary history of  lys2 . We suggest that the unique tree topologies of  lys2  are not due to an analytical artefact, but due to differences in the evolutionary history of genomes caused by positive selection of particular lineages.    Conclusion  This study showed the reliable species tree of the higher and lower taxonomy in the lineage of the  Fusarium  genus. Our ML tree clearly indicated 7 major clades within the  Fusarium  genus. Furthermore, this study reported differences in the evolutionary histories among multiple genes within this genus for the first time.

Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes