Abstract:The mitochondrial DNA control region (D-loop) of Siniperca chuatsi was amplified by PCR using a pair of specific primers. The sequences with the complete nucleotide control region from S.chuatsi mitochondrial was cloned and directly sequenced. The length of this region (Dloop) contained 833 bp nucleotides and the T, C, A and G contents were 30.4%, 20.4%, 33.7%and 15.5% respectively. The genetic diversity of S.chuatsi from the Nanhai, Guangdong; Huizhou, Guangdong; Nanchang, Jiangxi and Poyang Lake (Jiangxi) was analyzed. The results indicated, compared to Jiangxi S.chuatsi species, S.chuatsi species in Guangdong have a problem that the quality of species has low polymorphism. The polymorphism analysis has evaluated S.chuatsi’s heredity multiple levels, provides the scientific basis for S.chuatsi’s idioplasm protection, provides the genetics background material for development and utilization of S.chuatsi’s resources, in order to formulate corresponding resources conservation measures. Meanwhile it is significantly meaningful that the intensification of China’s main production area Guangdong Province’s S.chuatsi industry should be promoted to highly effective, highquality direction with sustainable healthy development.