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The species differentiation between Chamaecyparis formosensis, C. obtusa var. formosana, and C. obtusa, based on the composition of the leaf essential oils, was studied. The characterization of the oils by GC-FID and GC/MS analyses showed remarkable differences between these three essential oils. Cluster analysis (CA) and principal-component analysis (PCA) distinguished three groups of essential oils. The C. formosensis oil was dominated by α-pinene while those isolated from C. obtusa var. formosana and C. obtusa were characterized by high levels of (-)-thujopsene and α-terpinyl acetate, respectively. Moreover, the phylogenetic relationships of the genus Chamaecyparis were in agreement with previous findings based on morphological and molecular evidence. In addition, the essential oils from C. obtusa var. formosana could be classified into three chemical types, according to their different characteristic main compounds (β-elemol, (-)-thujopsene, and cis-thujopsenal). The biochemical correlations between the major constituents of the Chamaecyparis species were examined and their relationship is discussed., (Copyright © 2011 Verlag Helvetica Chimica Acta AG, Zürich.)