Seedlings and old trees of Scots pine in self-regenerating, old, virgin boreal forest in northern Sweden were compared in terms of the species composition of their associated ectomycorrhizal (EM) fungi. The natural regeneration of seedlings was mimicked by annual seeding for 10 yr (1986–1995) in intact field vegetation at three sites. In 1995, all seedlings were harvested, and 171 were examined for mycorrhizas. Twenty-five soil cores were taken in order to study the mycorrhizas on the established trees. Most short roots were mycorrhizal. Using mycorrhizal morphology and restriction fragment length polymorphisms (RFLP) analysis, we were able to distinguish 43 ectomycorrhizal taxa. Fourteen of these taxa were identified using a sporocarp and mycelial culture based internal transcribed spacer (ITS)-RFLP reference database, and another three were identified by mycorrhizal morphology. Cenococcum geophilum, Piloderma croceum and Suillus variegatus were present on the seedlings, irrespective of age, as well as on the old trees. At one forest, 23 ectomycorrhizal taxa were found as mycorrhizas, of which 10 occurred on both seedlings and old trees. These 10 species accounted for 92 and 73% of the mycorrhizas on the seedlings and old trees, respectively. A 3-yr survey of ectomycorrhizal sporocarps at the same site revealed 62 EM taxa. The degree of similarity between the composition of EM species reflected by sporocarps and by mycorrhizas, was low. Ectomycorrhizal species present in our ITS-RFLP database constituted 7.5–19% of the mycorrhizas on seedlings and old trees, whereas they constituted 80–95% of the total production of epigeous sporocarps. The unidentified taxa comprised 70–87% of the mycorrhizas. Our findings support the view that the species composition of mycorrhizas colonizing naturally regenerated seedlings in forests is similar to that of mycorrhizas colonizing surrounding trees. We suggest that the concept of the mycelial network be expanded in order to embrace both the significance of interconnections between different trees as well as the continuity or perpetuation of EM fungal communities.