Asia is the center of Tilia (Malvaceae) species diversity. However, the ectomycorrhizal (ECM) relations of Asian Tilia are scarcely studied. This study provides the first description of ECM communities of Tilia kiusiana, a rare tree endemic to southwestern Japan. Across the natural distribution of T. kiusiana, ECM fungal communities hosted by the species were investigated in three study sites: Hyōgo (H) and Yamaguchi (Y) on Honshu Island, and Ōita (O) on Kyushu Island. Using molecular methods, T. kiusiana was revealed to host a high diversity of fungi belonging to 25 ECM lineages (16, 17, and 14 lineages on sites H, Y, and O, respectively). The ECM communities of T. kiusiana and the previously studied endemic T. japonica were compared to the available data on other ECM tree genera in Japan, revealing that three Ascomycota ECM lineages (/genea-humaria, marcelleina-peziza gerardii, /tuber-helvella) show a preference towards Tilia hosts. While the total lineage richness did not differ among the compared host tree genera, Tilia communities exhibited higher effective lineage richness at higher (less sensitive to rare taxa) diversity orders. Despite their relative rarity, Tilia trees might play an important role in mixed forests: maintaining the diversity of ECM Ascomycota and potentially buffering the ECM fungal biodiversity loss in cases of ECM tree host diversity decline.