To investigate genetic diversity and structure of wild populations in the Yangtze River, a total of seventy-nine individuals from four wild populations (i.e., CS-Chishui River, NJ-Nanjing, YC-Yichang, and YY-Yueyang) were analyzed using the complete sequences of the mitochondrial markers Cyt b sequences were 1141 bp in length, and 26 haplotypes were detected. The Cyt haplotype diversity ranged from 0.685 (CS) to 0.924 (YC) and nucleotide diversity ranged from 0.176% (CS) to 0.285% (YY). Genetic distances within or between populations were both between 0.002 and 0.003. The whole D-loop sequences were 834-840 bp in length and 46 haplotypes were detected. D-loop haplotype diversity ranged from 0.754 (CS) to 0.990 (NJ) and nucleotide diversity ranged from 0.548% (CS) to 1.412% (YC). Genetic distances within populations were between 0.005 (CS) and 0.014 (YC), and from 0.008 to 0.012 among populations. The differences between these four populations of have not risen to the subspecies level based on the genetic distances. Analysis of molecular variance (AMOVA) with Cyt and D-loop sequences showed that most variance occurred within populations, suggesting that this is the main source of total variance.