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To add to knowledge of ectomycorrhizal (ECM) community structure on the roots of Pinus thunbergii seedlings in a Japanese coastal forest, we sampled naturally regenerated current-year and 1- to 5-year-old seedlings. We classified the 667 root tips on current-year seedlings and the 1,927 root tips on older seedlings into 13 phylotypes based on morphological and genetic analyses. Cenococcum geophilum, members of the families Clavulinaceae, Russulaceae, or Thelephoraceae or the genus Trichophaea, were indicated to be fungi forming P. thunbergii ectomycorrhizas. Among them, C. geophilum and Clavulinaceae sp. 1 were the most or second most dominant species. A species accumulation curve based on the number of samples nearly reached a plateau, with observed species richness equal to 11 species and the Jackknife2 and Chao2 richness estimators indicating 14 and 12 species …