Abstract: Objective To analyze the genetic characteristics of the hemagglutinin and neuraminidase genes of influenza A/H3N2 viruses isolated in Yancheng City from 2015 to 2017. Methods From 2015 to 2017, a total of 3 891 influenza-like specimens from the Yancheng Influenza Surveillance Hospitals and the influenza outbreak places were collected and sent to Yancheng center for disease control and prevention (CDC) for virus nucleic acids and virus isolation testing. After validation with serological tests, we selected twenty strains of influenza A H3N2 virus isolates to amplify their HA1 and NA genes through reverse transcription polymerase chain reaction (RT-PCR) assay. Results Basically, the clustering relationships and the branche patterns between HA1 and NA genes from the 20 Yancheng A/H3N2 virus strains were similar. The evolutionary distance of two Yancheng isolates(A/Jiangsu-YC/1474/2015 and A/Jiangsu-YC/1725/2015) with the two vaccine strains (A/Switzerland/9715293/2013 and A/Hongkong/4801/2014) were relatively close, however, the other 18 Yancheng isolates were clustered together with many recent domestic strains, which were far from the two vaccine strains (A/Switzerland/9715293/2013 and A/Hongkong/4801/2014). Because the antigen epitopes, receptor binding sites and glycosylation sites in the HA1 genes coding region of Yancheng isolates mutated at a certain degree, vaccine strain A/Switzerland/9715293/2013 was estimated to be less effective than the vaccine strain A/Hongkong/4801/2014 in protecting the influenza infection in Yancheng City from 2015 to 2017. About the catalytic residues and drug resistant sites of NA genes, all 20 isolates of Yancheng H3N2 influenza virus did not change. Conclusions Our results indicated that the HA1 and NA genes of influenza A/H3N2 viruses circulated in Yancheng City from 2015 to 2017 are changing gradually. The accumulation of these mutations would result in antigenic drift of influenza A/H3N2 viruses and increase the mismatch of the IFV field stains with the available vaccine strains, which might reduce the protective effect of flu vaccine.