The genetic structure and genetic variation of three populations of Coilia ectenes taihuensis in different lakes are investigated using the mitochondrial control region gene. Results show that the hapotype diversity(h) and mean nucleotide diversity(π) of the populations of different lakes are 0.9646 and 0.0097, respectively. 30 hapotypes were detected out of 45 individuals from the three populations. Only three of these haplotypes were shared among three lakes which contributed much to the genetic diversity. The AMOVA analysis and the pairwise F_st values revealed no significance among three populations of C. ectenes taihuensis. NJ and Bayesian analyses revealed that individuals of three populations formed three clades with poor support, but no clear relationships between haplotypes and geographical regions. We inferred that C. ectenes taihuensis populations in Lake Nansi originate from lakes in the Yangtze River by the ecological urgent water diversion in 2002.