The phylogenetic relationships of anastomosis groups (AG) of Rhizoctonia associated with Ceratobasidium and Thanatephorus teleomorphs were determined by cladistic analyses of internal transcribed spacer (ITS) and 28S large subunit (LSU) regions of nuclear-encoded ribosomal DNA (rDNA). Combined analyses of ITS and LSU rDNA sequences from 41 isolates representing 28 AG of Ceratobasidium and Thanatephorus supported at least 12 monophyletic groupings within Ceratobasidium and Thanatephorus. There was strong support for separation of Ceratobasidium and Thanatephorus, however, six sequences representing different AG of Ceratobasidium grouped with certain sequences within the Thanatephorus clade. Phylogenetic analysis of ITS sequence data from 122 isolates revealed 31 genetically distinct groups from Thanatephorus (21 groups) and Ceratobasidium (10 groups) that corresponded well with previously recognized AG or AG subgroups. Although phylogenetic analysis of ITS sequences provided evidence that several AG of Ceratobasidium may be more closely related with some AG from Thanatephorus, these relationships were not as strongly supported by bootstrap analysis.