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Background Only a few studies have investigated the bioactivity of the essential oils (EOs) of Chamaecyparis formosensisand C. obtusavar. formosana, which are endemic to Taiwan. The wood and leaf EOs extracted from C. obtusavar. formosanahad anti-inflammatory and antitermitic effects, respectively, and the twig EO extracted from C. formosensisinhibited the growth of Fusarium oxysporum, Pestalotiopsis funerea,and Ganoderma australe.Methods A poisoned food technique was used to evaluate the antifungal effects of wood and leaf EOs extracted from C. formosensisand C. obtusavar. formosanaon brown rot fungus, white rot fungus, and mold. A phytatray chamber assay was conducted to investigate the antifungal activities of the EOs in the vapor phase. Gas chromatography-mass spectrometry was used to examine the chemical constituents of both EOs.Results The leaf EO extracted from C. formosensisprimarily contained monoterpene hydrocarbons, whereas the leaf EO extracted from C. obtusavar. formosanaprimarily contained monoterpene and sesquiterpene hydrocarbons. The wood EOs extracted from C. formosensisand C. obtusavar. formosanaprimarily contained sesquiterpene hydrocarbons and oxygenated sesquiterpenes. These results indicated that the wood EOs had higher antifungal activity in the liquid phase, whereas the leaf EOs had higher antifungal activity in the vapor phase.Conclusion Wood EOs extracted from C. formosensisand C. obtusavar. formosanahave strong antifungal effects against Gloeophyllum trabeum, Lenzites betulina, Trametes versicolor, and Trichodermasp. Compared with wood EOs, leaf EOs have a greater inhibitory effect on mycelial growth in the vapor phase. In both the liquid and vapor phases, the EOs extracted from C. formosensisand C. obtusavar. formosanaserve as effective antifungal agents against pathogenic fungi. Further research is required to elucidate the mechanisms underlying the antifungal activities of EOs in different phases and explore their potential applications.