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A violet root rot fungus recently found in Japan was identified as Helicobasidium brebissonii. The fungus was compared with another violet root rot fungus, H. mompa, which is distributed throughout Japan, in terms of morphological characteristics of the basidiospores and the conidial state, sequences of rDNA ITS regions, and pathogenicity on carrot, sweet potato and apple rootstock. The two species were clearly discriminated by these features and the taxonomic status of both species is discussed.