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Abstract: Coilia ectenes is an important commercial fisheries species. In this study, the genetic diversity and population structure of ten Chinese populations of C. ectenes were investigated using cytochrome b (cytb) sequences of mitochondrial DNA (mtDNA). We sequenced the complete cytb gene of 279 individuals. One hundred and eleven polymorphic sites defined 97 distinct haplotypes. Haplotype diversity (Hd) ranged from 0.6433 to 0.9517 and nucleotide diversity (π) ranged from 0.16% to 1.23%. The Wuhan (WH) fish population had the highest π level. The genetic distances ranged from 0.16% to 1.26% within populations and from 0.18% to 2.66% between populations. The distances between the Fuzhou (FZ) population and other populations were greater than 2%, while the distance between the Lianyungang (LYG) and Taihu Lake (TH) populations was the smallest. The fixation index analysis indicated that there was significant genetic divergence among populations from different geographical groups. Both the neighbor-joining tree and median-joining network analysis of the haplotype data showed distinct patterns of phylogeographic structure. The hierarchical analysis of molecular variance (AMOVA) revealed that intra-group variation among populations (θ SC) was highly significant. The results of this study suggest that C. ectenes populations, especially geographically isolated groups, have developed significant genetic structures. In addition, tests of neutral evolution and mismatch distribution suggest that C. ectenes may have experienced a population expansion, possibly in the past 110,000years. [Copyright &y& Elsevier]