Hinoki-asunaro (Thujopsis dolabrata Sieb. et Zucc. var. hondai Makino) is a tree endemic in Japan whose seeds produce several terpenoids. We hypothesized that antifungal compounds in seeds might select for fungi on the root surfaces of T. dolabrata var. hondai seedlings. We examined seed and soil fungi, their sensitivity to methanol extracts of the seeds, the fungi on root surfaces of seedlings grown in Kanuma pumice (a model mineral soil) and nursery soil, and the frequency at which each fungus was detected on the seedling root surface. We calculated correlation coefficients between fungal detection frequency on root surfaces and fungal sensitivity to seed extracts. We also isolated from the seeds the antifungal compound totarol that selected for fungi on root surfaces. Species of Alternaria, Cladosporium, Pestalotiopsis, and Phomopsis were the most frequently isolated fungi from seeds. Mortierella and Mucor were the dominant fungi isolated from Kanuma pumice, whereas Umbelopsis and Trichoderma were the main fungi isolated from nursery soil. Alternaria, Cladosporium, Mortierella, Pestalotiopsis, and Phomopsis were the dominant fungi isolated from root surfaces of seedlings grown in Kanuma pumice, and Alternaria, Cladosporium, Pestalotiopsis, Phomopsis, and Trichoderma were the main root-surface fungi isolated from seedlings grown in nursery soil. The fungal detection frequencies on root surfaces in both soils were significantly and negatively correlated with fungal sensitivity to the seed extract. A similar correlation was found between the fungal detection frequency on root surfaces and fungal sensitivity to totarol. We conclude that totarol is one factor that selects for fungi on root surfaces of T. dolabrata var. hondai in the early growth stage.