Genetic relationships among the violet root rot fungi were studied by hyphal anastomosis and sequencing of the ITS-5·8S rDNA regions. Twelve isolates of Helicobasidium mompa, one isolate each of H. purpreum and H. compactum, two isolates of Helicobasidium sp., eight isolates of Rhizoctonia crocorum, and three isolates of R. violacea anastomosed in most combinations, resulting in the death of fused cells and adjacent cells. Phylogenetic analyses of the ITS-5·8S rDNA regions separated 31 violet root rot fungal isolates into five lineages: H. mompa from Japan and Korea; R. crocorum from Europe and New Zealand; H. purpureum, R. crocorum, and R. violacea from Europe; Helicobasidium sp. from Japan; and H. compactum from the USA. Within each lineage there was no more than one nucleotide substitution, and similarity ranged from 81·8% to 98·2% between lineages. The discrepancy between the results from the two methods are discussed in terms of the biological species concept in the complex.