The mitochondrial DNA control regions of Siniperca scherzeri Steindachner collected from the Yalujiang River, Yangtze River, Qiantangjiang River, Minjiang River and Xijiang River were amplified with PCR technique and sequenced. The result showed 112 nucleotide sites were variable among 818 bp length of homologous sequence and 20 haplotypes were found in all 36 individuals. Each population owned the different haplotypes, some population specific sites were also found in the populations from the Yalujiang River and Qiantangjiang River. Molecular tree constructed by NJ method showed all the individuals from the Yalujiang River, Yangtze River, Qiantangjiang River and Xijiang River populations, respectively, could be clustered as one group independently, except that the individuals from the Minjiang River were mixed with those of the Yangtze River and Xijiang River. These showed there were significant genetic differences among the 5 populations of S. scherzeri in China.