The fishes of smelt genus Hypomesus lives in fresh water, brackish water and coastal seas，distributes in the Northern Hemisphere. Now, the Japanese smelt H.nipponensis and the pond smelt H.olidus are the common species and mainly distributed in the northeast region in China. Their body are small with silvery white. The life span of the fishes is short and theirs age of sexual maturity is above 1 year and they dies after spawning. They have strong adaptability and have been transplanted widely in China as the important commercial fishes. However, it is strange that there still exist disputation so far on which species of Hypomesus ever been transplanted widely in China. In this study, transplanted smelt collected from seven places locating in Heilongjiang , Xinjiang and Yunnan province are identified using CO I gene, which is a popular DNA barcoding for species identification in the world. Comparative analysis showed that CO I gene sequence from all above collected somelts shared more than 99% similiarity with that from H. nipponensis, which was published on the webs of GenBank and DNA barcoding Center. Genetic distance within each group and pairwise distance between transplanted smelt and H. nipponensis both ranged from 0.1% to 0.3%, and were rather smaller than those genetic distances between transplanted smelt and other species of Hypomesus (all more than 10%). The topology of each final trees further revealed that all individuals of transplanted smelt and H. nipponensis formed a strong monophyletic group. Taken together, these results all showed that the transplanted smelt were Japanese smelt H. nipponensis. In addition, even the genetic differentiation in transplanted smelt populations was not significant (P=0.06647＞0.05）, six populations of transplant Japanese smelt endured somewhat selection pressure of environment based on Tajima's D value. Median-joining haplotype network for Hypomesus 7 transplant populations can not tell us too much about their genetic relation and the transplant routes. Cross-transplant or/and multi-transplant might be the reason.