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The Chinese toad Bufo gargarizans has an extensive range, covering nearly all of China. This study addresses the population genetic structure of this toad and the relation to geographic location. Partial sequences of the mtDNA control region were obtained from 14 populations, 29 haplotypes were defined, and 73 variable sites were found, including 66 parsimony informative sites. All population genetic analyses indicated no clear geographic pattern in the distribution of haplotypes. The genetic divergence between the populations was significant. Phylogeographic analyses suggested that past fragmentation and/or long-distance colonization seemed to have shaped the present-day distribution of the haplotypes of B. gargarizans.