The number of Pheasant-tailed Jacana (Hydrophasianus chirurgus) in Taiwan has been reduced and habitats decreased because of human activities in many years. From a conservation perspective, the genetic diversity of this bird became an important subject. The control region in mitochondrial DNA was used as a gene marker to investigate the genetic variation amoung populations of Hydrophasianus chirurgus from Taiwan, Goungdong, and Thailand. An 1182-bp nucleotide sequence was amplified from 34 individuals. Six variable sites and seven haplotypes were found in the control region, and the observed haplotypes were similar in all samples. Low genetic divergence and high degree of gene flow were estimated among three populations. However, this conclusion need more samples of individuals to be proved.