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The genus <i>Chamaecyparis</i> comprises seven species (<i>C. formosensis</i>, <i>C. hodginsii</i>, <i>C. lawsoniana</i>, <i>C. nootkatensis</i> (<i>Callitropsis nootkatensis</i>), <i>C. obtusa</i>, <i>C. pisifera</i>, and <i>C. thyoides</i>). Accurate species identification is necessary for proper use and economic value of wood. Species identification of woods is generally based on anatomical analysis; however, <i>C. obtusa</i> and <i>C. pisifera</i> wood have similar microscopic morphology, which makes species identification impossible. Therefore, the molecular identification of species in wood of the genus <i>Chamaecyparis</i> is required. In this study, six candidate DNA barcode genes (<i>trnP-GGG</i>, <i>ycf1</i>b, <i>clpP</i>, <i>accD</i>, <i>ycf2</i>, and <i>rps16</i>) in the chloroplast of <i>Chamaecyparis</i> were identified with nucleotide diversity values higher than the arbitrary value of 0.02. Each gene was evaluated for species identification using phylogenetic analysis by genes registered at NCBI (42 sequences each for <i>trnP-GGG</i>, <i>ycf1</i>b, <i>clpP</i>, <i>accD</i>, and <i>ycf2</i>, and 50 sequences for <i>rps16</i>). The genes <i>trnP-GGG</i>, <i>clpP</i>, and <i>rps16</i> could not be distinguished between <i>C. pisifera</i> and <i>C. formosensis</i>. However, <i>ycf1</i>b, <i>accD</i>, and <i>ycf2</i> could be distinguished between all <i>Chamaecyparis</i> species. These results suggest the use of the chloroplast genes <i>ycf1</i>b, <i>accD</i>, and <i>ycf2</i> as DNA barcodes for species identification in <i>Chamaecyparis</i>, including <i>C. obtusa</i> and <i>C. pisifera</i>, based on the reported genetic information to date.