There has been conflicting debate over many years regarding the trophic status of Matsutake. Here we examined the morphology, structure and ultrastructure of Pinus densiflora roots collected from a Tricholoma matsutake Shiro within a pure Japanese red pine stand. Molecular investigations (PCR–RFLP analyses) indicated that T. matsutake was the highly dominant fungus within both the Shiro and the colonized root tips, suggesting that reported root morphology modifications can be attributed to T. matsutake infection. The external morphology of Matsutake-colonized roots is consistent with previous descriptions. The presence of extraradical mycelium, mantle, and intracortical Hartig net hyphae indicates clearly that T. matsutake forms an ectomycorrhizal association with P. densiflora in naturally occurring Shiros. The elucidation, for the first time, of the Hartig net ultrastructure at the host–fungus interface provides further and convincing evidence of a conventional ectomycorrhizal association. The progressive blackening, observed from base to tip in dominant mycorrhizal types, due to increased deposition of polyphenol and subsequent necrosis, appears to be a result of infection. However, the presence of highly nucleated vascular tissue indicates the viability of the vascular cylinder in these roots bearing necrotic cortices. Such a preponderance of black necrotic cortical tissues among colonized roots may reflect some atypical behaviour of T. matsutake.