We determined 35 complete mitochondrial control region sequences of Coilia nasus from 3 populations,which included Jiuduansha area(JJ)in Yangtze River estuary,Qiantangjiang River estuary(QT)and Zhoushan Island(ZS),to analyze their sequence variation and genetic structure.Sequence lengths of the control region in individuals of C.nasus were 1 214-1 291 bp,which revealed that the control region sequence of C.nasus had length polymorphism.Sequence length polymorphism caused mainly by one or two times of 38 bp of "CTA TGT ATT ATA TTA CAT ATA TTA TGG TAT AGT ACA TA" segment repeats.Genetic structure analysis showed a high level genetic diversity of C.nasus(h=0.998 3,π=0.026 2),which indicated that C.nasus had high evolutionary potential.The high level of N_m values(9.90-40.62)and very low F_ST values(0.012-0.053),the average K 2-P distances,as well as the AMOVA analysis all revealed that the C.nasus around Yangtze River estuary had no obviously geographical differentiation.However,the phylogenetic tree estimated by neighbor-joining(NJ)methods indicated that the individuals of C.nasus formed two monophyletic lineages,and the two lineages without correlation with geographical populations.Based on molecular clock theory,the two lineages might share a common ancestor approximately 35-47 thousand years ago.