Abstract：Nucleotide sequences of 16S rRNA, Cyt b, and D-loop of mitochondrial DNA (mtDNA) for nine domestic populations and two wild populations of common carp (Cyprinus carpio) were amplified using PCR techniques and their genetic variability and phylogenetic relationships were analyzed. Thirty-two nucleotide variable positions, 21 parsimony-infomative positions and 16 haplotype were detected in 1 457 bp length sequence among the strains. Phylogenetic trees were constructed from the three different genes sequences as well as the combination sequences by NJ and MP method. There were no contradictions between these phylogenetic trees. The phylogenetic trees were all divided into two branches which Beier Lake wild carp (BE) was singleness and the others were clustered into one group. And a more particular phylogenetic relationship was obtained using D-loop sequences. Moreover, there were no contradiction between the phylogenetic trees constructed by combination sequences and different gene sequences, respectively. The estimated divergence time among breeding different populations was about 3.03 ×104～1.21×105 years ago. As a result, one variable position of 16S rRNA, 4 variable positions of Cyt b gene and 14 variable positions of D-loop region could be used as (SNP) to identify the different strains or wild populations. It was proved that the nucleotide sequences of mtDNA could be used in the identification of strains.
