The mitochondrial CR and Cyt b gene segments of 24 Squaliobarbus curriculus from Yangtze River and Pearl River were amplified by PCR technique and sequenced.Analysis of the 1 345 bp combined mtDNA CR and Cyt b gene sequence showed that there were 23 haplotypes,22 single-base mutation and 102 parsimony-informative sites.In the 139 variable sites,there were 100 transition sites,30 transversion sites and 14 insertion/deletion sites.The content of A+T (61.5%) was much higher than that of C+G (38.5%).The genetic variation among the 4 populations ranged from 0 to 7.43%.The haplotype diversity(H),mean number of pair-wise differences (K±SD) and nucleotide diversity (π) were 0.977 8,17.271 0 and 0.002 7,respectively,suggesting high genetic diversity.There were significant genetic differences of FST values between Yangtze River and Pearl River,but there were no genetic differences within the same river.The result of molecular phylogenetic tree constructed by NJ and ML methods and median joining network of 23 haplotypes also supported that point.Analysis of molecular variance (AMOVA) showed that the genetic differentiation among four populations was caused by genetic variation between Yangtze River and Pearl River and no genetic differentiation existed between populations within the same river,which further supported the FST result.The obvious genetic differentiation was mainly attributed to the reproductive isolation caused by the geographical isolation between Yangtze River and Pearl River.But,in the same river system,there was no genetic differentiation between different populations because of wide genetic communication caused by the “semi-immigrations” behavior of S.curriculus.