Spinibarbus caldwelli was an endemic species to China, and its germplasm protection and resources utilization had become more and more concerned. To know its genetic diversity and differentiation, the mitochondrial DNA D-loop was amplified and sequenced for 148 individuals from four regions of Pearl River and Yangtze River Basin. Altogether 9 variable nucleotide sites existed among the aligned sequences of 748 bp, and 8 haplotypes were found within 148 individuals. The average nucleotide diversity (Pi) was high 0.00297, while haplotype diversity (Hd) was 0.706. The average genetic distance was 0.00298, most value occurred between LJ and CL populations, and small value occurred between HJ and QZ populations.
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