Binucleate Rhizoctonia endophytes from the roots of nursery-grown Pinus sylvestris (Scots pine) seedlings and the orchid Goodyera repens from Scots pine forests were characterized on the basis of morphological characters, anastomosis group membership and PCR-assisted ribosomal DNA fingerprinting. Common hyphal and colony morphological traits displayed by the Finnish binucleate Rhizoctonia isolates and a range of Canadian orchid root endophytes enabled them to be placed in the anamorphic genus Ceratorhiza. Five main anastomosis groups were identified and included groups that contained different combinations of Scots pine, G. repens and Canadian Ceratorhiza spp. isolates. Two Scots pine root endophytes anastomosed with a phytopathogenic Japanese tester isolate, confirming their membership of anastomosis group I, which is known to include the teleomorphic species Ceratobasidium cornigerum. Hierarchical cluster analysis of RFLPs in the internal transcribed spacer of ribosomal DNA enabled the division of isolates into one of five RFLP groups. The RFLP and anastomosis groupings were closely correlated; isolates within each of four RFLP groups, which shared 100% RFLP identity, anastomosed in the cross-pairing anastomosis group tests. However, all represented different vegetatively compatible populations (clones) because the diagnostic killing reaction, a cellular vegetative incompatibility response, was identified at hyphal fusion junctions. These findings indicate a high degree of intraspecific variation within Ceratobasidium cornigerum, which includes isolates able to enter into either mutualistic or pathogenic root association with susceptible host plants. The common anastomosis group/RFLP groupings identified also strongly support the hypothesis that conifer tree roots can act as large inoculum reservoirs for these orchid endophytes, allowing the development of inter-plant connections, via commonly shared hyphal linkages, in boreal forest ecosystems.