Abstract: The control region (D-loop) of Anabarilius grahami was amplified by PCR amplification with a pair of specific primers. The sequence with the complete nucleotide control region from A. grahami mitochondrial was cloned and directly sequenced. The length of this region (D-loop) contained 930 bp nucleotides and the T, C, A and G contents were 29.8%, 22.5%, 33.0% and 14.7% respectively. The mtDNA control region of A. grahami could be partitioned into three domains, namely, the termination associated sequence domain, the central conserved sequence domain and the conserved sequence block domain. The extended termination associated sequence (ETAS), two conserved blocks (CSB-F, CSB-D) in the central conserved sequence block domain and three conserved sequence blocks (CSB1, CSB2, CSB3) in the conserved sequence block domain were successfully identified and their homology compared with other fish. The genetic diversity analysis of A. grahami from the Endangered Fish Breeding Center (EFBC) of the Kunming Institute of Zoology (KIZ), Mingxing Fish Cave (Jiangchuan), Niumo Village (Jiangchuan) was analyzed. The result indicated a very low genetic divergence between two natural populations, and the genetic diversity of the population from EFBC was much higher; they had recovered better than others.