Genetic diversity and structure were investigated to explore the phylogeography and evolution of from five different river systems, including Wusuli River, Yangtze Rive, Heilongjiang River, Yalu River and Mudan River. The mtDNA control region was used to analyze genetic differentiation of eight geographical populations (=42) in this study. Results showed that 26 variation sites existed in a 404 bp sequence with variation rate of 6.43% and average nucleotide diversity of 0.011 5. The sequence information identified 18 haplotypes in the control region gene. Eight geographical populations were evolved through a mode of center outward radiation based on DWRHT1 and DWRHT2 haplotype. AMOVA analysis showed that the variation rate was 59.29% within populations, 23.50% among populations from the same river system and 17.20% among populations from the different river system. There was significant difference within different populations, among populations from the same river system and populations from different river systems ( of control region sequence analysis among populations showed that there was significant difference among several populations from the same river system. Cluster analysis showed that maximum-parsimony method (MP) and maximum likelihood ratio method (ML) results were basically consistent, which suggested that most individuals from HRJY and YRSC population clustered together and individuals from YRLJ population clustered into a single branch. Meanwhile, cluster analysis results were found to be consistent with haplotype parsimony network analysis. These results suggested abundant genetic diversity existed among populations. However, the population size was decreased due to environmental pollution and overexploitation in recent years. In addition, H. labeo from other river systems had evolved to different directions based on haplotypes from Heilongjiang River and formed their unique haplotypes during the long-term evolution and geographical isolation.