Coreoperca is a group of freshwater fishes endemic in East Asia.To study the genetic structure and differentiation of C.whiteheadi in China,the sequences of mitochondrial DNA control region of 34 samples,collected from Yangtze River,Qiantangjiang River,Xijiang River and Nandujiang River,respectively,were analyzed by PCR and sequencing methods.Among the 838 bp length homologous sequences,81 variable sites(9.67%) were detected.4 haplotypes were identified,each belonged to one single population.No haplotype was shared among four populations while each population had some fixed diagnostic sites.The nucleotide divergence(Dxy) among populations was 0.360%-8.043%,while Nandujiang population showed significant divergence with the others.The fixation index(Fst) calculated by the analysis of molecular variance(AMOVA) reached 1.000(P<0.001).NJ tree of the control region suggested that the 4 populations were divided into two clades: one clade included Nandujiang population,another clade comprised Yangtze,Qiantangjiang,Xijiang populations.These results suggested that genetic variance of C.whiteheadi is relatively low and the genetic differentiation among the four populations is significant;the Nandujiang population diverged distinctly from the other three populations.