The mitochondrial DNA control region of Siniperca chuatsi stocks collected from the Lake Dongting (DT), Lake Poyang( PY), Qiupu River(QP) and Lake Taihu(TH) of the Yangtze River were amplified with PCR technique and DNA sequencing.The result showed 36 nucleotide sites were variable among 785 bp length of homol- ogous sequence.A total of 19 haplotypes found in all 42 individuals could be grouped into two groups, type Ⅰ and type Ⅱ, of which 6 sites were significant differentiated.Nucleotide at the 6^th, 8^th, 1^th, 25^th, 35^th variable position was G, C, G, A, C in type Ⅰ, while A, T, A, G, T in type Ⅱ.Regular geographical changes of the haplotype distribution was not observed in different sections along the Yangtze River except for TH possessing only type Ⅱ haplotypes.Sequence divergence of control region of S.chuatsi within DT, PY, QP, TH stock was 0.5%, 1.0%, 0.6%, 0.5%, respectively, Sequence divergence among the 4 populations was 0.6%- 0.9%.Molecular tree constructed by NJ method showed the individuals of the different stocks eouldn’t be clustered as one independent group and mixed to each other.The lower divergence among 4 stocks suggested they maybe belong to one single the Yangzte River population.These results could be served as base for further study on the genetic diversity of S.chuatsi, genetic conservation and utilization of the Yangtze River population.