In order to find new utilization method of woody wastes, we examined the bioactivities of extracts from branch heartwood of Chamaecyparis obtusa (hinoki) and compared to extracts from trunk heartwood. The bioactivities examined were antifungal activities against four fungi (Trametes versicolor, Fomitopsis palustris, Trichoderma virens, Rhizopus oryzae), and bioassay with brine shrimp (Artemia salina) which shows any allelopathic activities not measurable with fungi. Antifungal activities were observed in the hexane and ethyl acetate extracts of branch and trunk heartwood. The hexane and ethyl acetate extracts of branch and hexane extract of trunk showed strong lethality against brine shrimp. The yields of the active extracts of branch were much more than that of trunk. The identified compounds in the active extracts of branch were germacra-1-(10),5-dien-4b-ol, t-cadinol, t-muurolol, hinokiresinol, and hinokinin. Hinokiresinol and t-muurolol showed strong antifungal activities. Hinokiresinol showed bioactivities against T. virens, R. oryzae and brine shrimp. Germacra-1-(10),5-dien-4b-ol was lethal to brine shrimp. Germacra-1-(10),5-dien-4b-ol and hinokiresinol were minor components in trunk heartwood, but major components in branch. These qualitative and quantitative results suggest that the branch heartwood could be a valuable chemical resource because it contains large amounts of antifungal and allelopathic compounds.