Abstract: In order to identify the relationship between geographic subdivision and population genetic structure due to habitat loss and fragmentation, the complete sequenes of the mitochondrial control region from 28 Chinese giant salamanders collected from Yangtze River Region (Hunan and Shaanxi), Yellow River Region (Henan) and Pearl River Region (Guangxi) were sequenced. According to the analysis of Clustal X, MEGA2.0, DnaSP4.0 and Arlequin1.1, 64 nucleotide sites were variable, including 6 transitions, 2 transversions and 11 insertions/deletions in the complete D-loop gene sequence (771 bp). A total of 27 haplotypes were identified and the average genetic distance among all these haplotypes was 1.32%. Furthermore, the results showed that all three geographic regions exhibited low levels of nucleotide diversity and haplotype diversity, in which the two indexes of Yangtze River were the lowest. The results also presented that there was significantly distinctive geographic phylogeography between Pearl River Region and Yangtze River Region, between Pearl River Region and Yellow River Region (all P<0.001), but no obvious subdivision between Yangtze River Region and Yellow River Region (P>0.05). In addition, and the genetic variation within and between regions was 99.31% and 0.69% respectively, which means the genetic variation mainly happens within the geographic region and gene flow among the geographic regions was comparatively frequent. At last the phylogenetic tree analysis (NJ method and MP method) demonstrated that all the haplotypes could not be clustered to three geographic clades, but appear disordered distribution pattern.