Genetic diversity and genetic differentiation between Coilia ectenes and Coilia ectenes taihuensis have been investigated at the mtDNA level. Sequences analysis of cytochrome b (cytb) gene segments amplified by PCR was used. Five different haplotypes were detected between the populations studied. The haplotype diversity of C. ectenes and C. e. taihuensis were 0.9000 and 0.7000，respectively. The nucleotide diversity of C. ectenes and C. e. taihuensis were 0.3763% and 0.4301%, respectively. An hierarchical analysis of molecular variance (AMO-VA) showed that very low levels of genetic partitioning, with 0.00% of the total variation attributed to between population differences, and lack of genetic structure. Our results supported that C. e. taihuensis is a geographical population of C. ectenes; their difference has not risen to subspecies level.