Abstract：Coreoperca is a group of freshwater fishes endemic in East Asia. To study the genetic structure of different geographical populations of C. whiteheadi in China, the genetic variation of 65 samples, collected from Yangtze River (YZ), Qiantangjiang River (QT), Xijiang River (XJ) and Nandujiang River (ND), was analyzed by the AFLP technique. 10 primer combinations generated 1131 bands with 603 polymorphic bands; the average proportion of polymorphism was 53.32%. However, the proportion of polymorphism, genetic diversity and Shannon index within the YZ, QT, XJ and ND population was quite low. The genetic distances among the mainland populations of YZ, QT and XJ were small (0.098～0.189), whereas the distances between ND with the mainland populations were large (0.507～0.568). The analysis of molecular variance (AMOVA)showed the genetic ifferentiation among these populations was significant (FST = 0.972). NJ tree suggested that 4 populations could be divided into two clades: one clade included YZ, QT and XJ populations, another clade comprised of ND population. C. whiteheadi lives in the upper section of streams with a small population, the poverty of its gene bank may result in low genetic diversity within population. Meanwhile, lack of genetic flow among different populations and occurrence of random genetic drift within population have caused their divergence.
