Abstract: In this study, the complete fragment of the mitochondrial DNA control region were amplified using the genomic DNA of Dongtingking crucian carp (Carassius auratus Dongtingking variety) and Pengze crucian carp (Carassius auratus of Pengze). The PCR products were ligated and sequenced to the plasmid of pMD18-T Vector by the method of direct cloning, and then, the base composition, variation, sequence structure and phylogeny of the mitochondrial DNA control region were compared and analyzed among seven strains of Carassius auratus (Dongtingking crucian carp, Pengze crucian carp, crucian carp, Red crucian carp, Japanese crucian carp, Silver crucian carp clone A and D). In the seven strains of Carassius auratus, the percentages of average base compositions of the mitochondrial DNA control region were A (32.7±0.16)%, C (20.4±0.37)%, G (14.1±0.08)% and T (32.8±0.36)%, respectively, the sequences percent divergences were between 0—5.7%, the highest percent divergence (5.7%) was between Red crucian carp and Japanese crucian carp, and the lowest percent divergence (0) was among Pengze crucian carp, Silver crucian carp clone A and D. The percent divergence between Dongtingking crucian carp and Japanese crucian carp was 5.6%, which was 2.2% among Dongtingking crucian carp and Pengze crucian carp, Silver crucian carp clone A and D, 0.8% between Dongtingking crucian carp and Red crucian carp, and 0.7% between Dongtingking crucian carp and crucian carp. Compared with the mitochondrial DNA control region in mammalian and other fishes, the extended terminal associated sequences (ETAS), central conserved sequence blocks (CSB-F, CSB-E, CSB-D), conserved sequence blocks (CSB-1, CSB-2, CSB-3) and putative promoters of the mitochondrial DNA control region in the seven strains of Carassius auratus were observed. Analysis of the sequences percent divergences and phylogeny indicated that the Dongtingking crucian carp had a extremely close relationship with crucian carp and Red crucian carp, taking the second place with Pengze crucian carp, Silver crucian carp clone A and D, and had a farthest relationship with Japanese crucian carp. Moreover, the consistent similarity and percent divergence of the mitochondrial DNA control region among Pengze crucian carp, Silver crucian carp clone A and D demonstrated that they were the same strain of Carassius auratus.