We found significant differentiation between rock carp populations collected from eight geographical locations. Moderate
to high levels of genetic differentiation were observed among the main stream populations and among the tributary populations,
and between the large river populations and the small river populations, except for the differentiation between the
WZ and XS populations. However, Song et al. (2014) and Zhang et al. (2008) found that the genetic differentiation among large
river populations were smaller than those among the small river populations. The reason for the differences may be that the
total genomic DNA of samples in the present research were scanned by AFLP markers and more signals were detected, while
microsatellite markers only examined short tandem repeat sequences. The construction of forty thousand dams on the
Yangtze River and its tributaries has caused fragmentation of this fish's habitats. Rock carps in the upper reaches of the
Yangtze River are unable to migrate freely into the spawning grounds. The dams act as a barrier to the exchange of genes
between P. rabaudi populations and the water temperature, water quality, hydrography and topography in the fragmented
habitats are considerably different. This may have caused the fish to differentiate. However, we did not observe a distinct