Abstracts Capricornis swinhoei is one of the indangered wild animals in Taiwan. The objective of this study is using molecular biology and morphology methods to analyze the genetic diversity, observed population structure, differentiation and biogeographic relationships among the population of Capricornis swinhoei. Samples used in this study were collected from the Central Mountains located in Taiwan. DNA sequences (1099 bp) from the mitochondrial DNA (mtDNA) control region, D-loop, were used to test the phylogeographic relationships among the Capricornis swinhoei. A phylogenetic tree was constructed on the basis of GCG-Seq Web and MEGA softwares. In addition, distance analyses, neighbor-join, and maximum parsimony to resolve these phylogenetic relationships were performed. The C. sumatraensis and C. crispus sequence were also determined and used as the outgroups. Our findings clearly demonstrate that Capricornis swinhoei can be clustered into two groups, north and south groups, and consistent with the truth of geographic isolation. The data obtained from this study may facilitate the program of wildlife conservation in Taiwan.