Brown-eared Pheasant (Corossoptilon mantchuricum) is a critically endangered endemic species, listed in the national first-class protected bird in China. Since its population size is believed to be declining because of ongoing habitat loss, hunting and other human activity disturbance. For geographical barrier (Yellow River) and natural vegetation destruction (Vegetation of Taihang Mountain), Brown-eared Pheasant has formed three isolating populations in its distribution area including western Shanxi, north-western Hebei, western Beijing and central Shaanxi. Moreover, gene flows through these populations was obstructed. In order to protect the genetic resources of Brown-eared Pheasant and evaluate its genetic diversity at the molecular level, the complete mitochondrial DNA D-loop sequences of 20 Brown-eared Pheasants from Pangquangou Natural Reserve and Taiyuan Zoo were cloned and sequenced, respectively. These sequences were aligned to determine the polymorphic loci and the number of haplotypes by Clustal X, DnaSP4.0 and Mega3.1. In addition, the nucleotide diversity(π) and haplotype diversity(h) were calculated by the softwares above. The genetic variation of Brown-eared Pheasant between Pangquangou Natural Reserve and Taiyuan Zoo in Shanxi was analyzed, and the genetic diversity and genetic structure of the populations of Brown-eared Pheasant were investigated. The results showed that the lengths of mitochondrial DNA complete D-loop sequences of the Brown-eared Pheasant were between 1236-1237bp, the average base contents of A，T, G and C were 31.0％, 26.8％, 27.5％ and 14.8％，respectively，and the average content of A+T(57.8％) was higher than G+C(42.3％)．There were 26 transitions or transversions (1 insertion or deletion site was excluded) including 25 single nucleotide mutation sites and 1 parsimony informative site. According to the variations among the sequences，13 haplotypes were identified with 1-7 variation loci. 11 of them occurred in a single individual and 2 were shared haplotypes. The haplotype diversity (h), nucleotide diversity (π) and genetic distances estimated from mtDNA D-loop region within each population of Brown-eared Pheasant from Taiyuan Zoo and Pangquangou Natural Reserve in Shanxi varied from 0.911-0.933, 0.002-0.003, and 0.002-0.003, respectivly. The Neighbor-Joining molecular phylogenetic tree of mtDNA D-loop in the 2 captive Brown-eared Pheasant groups in Shanxi was constructed according to the 13 haplotypes. The NJ tree showed that the phylogenetic relationship of the Brown-eared Pheasant individuals was not correlative to their geographical locations.The differences between the two populations on the two genetic diversity parameters were not statistically significant, which meaned that there were no significant genetic differences occurred in the two populations, and there were gene flows between the two populations. These results strongly proved that the population of caprive Brown-eared Pheasant is in poor genetic diversity status.