Coilia nasus occurs as two different ecotypes in Yangtze River. To investigate the cause of the difference between population structures, we performed molecular clone and transposon displaying technology to obtain a novel Tc1-like transposon, named Cn-Tc1, from C. nasus. Cn-Tc1 with full length of 1 896 bp is the first Tc1-like transposon reported in Engraulidae fishes. Cn-Tc1 itself harbored an insertion of Tc1-like transposon of 1040 bp, suggesting that burst of Cn-Tc1 occurred in genome for several times. The lengths of inverted terminal repeats at the 5'and 3'ends of Cn-Tc1 were 64 and 83 bp, respectively. The sites at the insertions have a "TATA" motif. The predicted transposase showed a conserved DNA-binding structure, indicating that maybe Cn-Tc1 has potential for transposition. GC contents of the flanking sequence are higher than that of AT, showing an uneven distribution. A real-time PCR method was used to calculate the copy numbers of Cn-Tc1 in different populations including Jingjiang (JJ) in Jiangsu province, Xiangshan (XS) in Zhejiang province, Dongting Lake (DT), Poyang Lake (PY), Taihu Lake (TH), and Chongming (CM) in Shanghai. The copy numbers per haploid genome are 3.140×10³, 2.992×10³, 6.876×10³, 5.205×10³, 5.531×10³, 3.046×10³, respectively. With One-Way ANOVA analysis, there is no difference among XS, CM and JJ. When the three populations incorporated into one group of the migration, the difference among the group and other populations is significant. There is no difference among PY, TH and DT, but when incorporated into one group of the residence, the difference between the residence and the migration is significant. Our results indicated that the mutation of genetic structure caused via Cn-Tc1 facilitated the adaptive evolution of C. nasus populations by natural selection of genetic mutation.