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Coilia ectenes is a commercially important fishery species. In this study, genetic diversity and population structure of C. ectenes were examined by using mitochondrial DNA control region sequences in 246 individuals sampled from 10 localities in China. One hundred and ninety-five polymorphic sites defined 184 distinct haplotypes, revealing a moderately high haplotype diversity (Hd) and a relatively low nucleotide diversity (π) in the 10 localities. An excess of unique haplotypes at most sample locations were detected, which might influence the genetic structure of the C. ectenes populations. Hd ranged from 0.939 to 1.000 and π ranged from 0.26% to 1.15%. The Dongting fish population had the highest π level. The genetic distances ranged from 0.26% to 1.03% within populations and from 0.56% to 4.90% between populations. The distances between the Fuzhou (FZ) population and other populations were mostly >4.8%. Neighbor-joining tree indicated distinct patterns of phylogeographic structure among haplotypes from FZ population and those from other populations. Analyses of molecular variance and Fst statistics suggested that the divergence existed among populations from 10 localities, indicating that gene flow might be restricted among those regions, despite the wide dispersal. In addition, neutral tests and analysis of mismatch distribution suggested that C. ectenes might have undergone a population expansion. Our study revealed the extant population genetic diversity and structure of the C. ectenes, and was in favor of the related fishery management issues including fishery stock identification and conservation. [ABSTRACT FROM AUTHOR]