In this study antifungal activities of essential oils from different tissues of Japanese cedar (Cryptomeria japonica D. Don) against four wood decay fungi and six tree pathogenic fungi were investigated. In addition, the yields of essential oils obtained by water distillation were compared and their constituents determined by GC-MS analyses. The yield of essential oils from four tissues of Japanese cedar is in the decreasing order of leaf (27.38 mL/kg) > bark (6.31 mL/kg) > heartwood (3.80 mL/kg) > sapwood (1.27 mL/kg). Results obtained from the antifungal tests demonstrate that the essential oil of Japanese cedar heartwood used against Laetiporus sulphureus and Trametes versicolor and sapwood essential oil used against L. sulphureus had strong antifungal activities at 500 mug/mL, with IC50 values of 39, 91, and 94 mug/mL, respectively. Besides, the essential oils of Japanese cedar heartwood used against Rhizoctonia solani, Collectotrichum gloeosporioides, Fusarium solani, and Ganoderma australe had strong antifungal activities at 500 mug/mL, with IC50 values of 65, 80, 80, and 110 mug/mL, respectively. GC-MS analyses showed that the sesquiterpene hydrocarbon compounds dominate in the essential oil from Japanese cedar heartwood, amounting to a total percentage of 82.56%, with the major compounds of delta-cadinene (18.60%), isoledene (12.41%), and gamma-muurolene (11.82%). It is proposed that the excellent antifungal activities of Japanese cedar heartwood essential oils might correlate with the presence of these compounds.