The mitochondrial DNA Cyt b of 31 Siniperca scherzeri
collected from the Yalujiang River, Haihe River, Yangtze River, Qiantangjiang River, Minjiang River and Xijiang River were amplified and partially sequenced using the PCR technique. The results showed that 78 nucleotide sites were variable along 781 bp length of homologous sequence (9.6%), base substitutions happened mostly at the third codon position, and sixteen haplotypes were detected in 31 individuals. Genetic distances between the Yalujiang, Haihe population and the Yangtze, Qiantangjiang, Minjiang and Xijiang population were higher. The analysis of molecular variance (AMOVA) supported the conclusion that there was significant genetic differentiation between these six geographical populations (FST
=0.9307, P<0.01). A neighbour joining tree showed that the Yalujiang and Haihe population formed the northern clade and the Yangtze, Minjiang and Xijiang populations formed the southern clade. The Qiantangjiang population formed an independent clade instead of merging into the southern clade. The phylogenetic relationship revealed by the Cyt b sequence was not consistent with the species' geographical distribution patterns.