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The genera Aspergillus, Penicillium and Fusarium contain many mycotoxin producers and the identification and classification of these genera are confused because they lack distinct morphological character for each species. New taxonomic criteria for these genera are needed. The sequences (402 bp) of mitochondrial (mt) cytochrome b gene from these genera were determined and the phylogenetic relationship was analyzed.The phylogenetic tree based on cytochrome b (amino acid sequences) showed that Zygomycota, Ascomycota, Basidiomycota, Ascomycetous yeasts, Basidiomycetous yeasts and Schizosaccharomyces branched at early period in the evolution, respectively.The relationship in the genus Aspergillus based on cytochrome b showed that A. clavatus belonged to the subgenus Clavati was placed in cluster of subgenus Fumigati. A, terreus and A. flavipes separated from other species of subgenus Nidulantes, and they were placed in the cluster of subgenus Circumdati.Aspergillus section Flavi, including aflatoxin producers, were divided into 6 DNA types. A. sojae has individual sequence, different from that of A. parasiticus, in spite of the same conidial wall texture.