Abstract: Objective To study the epidemiological characteristics and variation of the influenza A(H1N1)pdm09 virus. Methods The throat swabs were collected from patients with influenza-like illness(ILI) in sentinel surveillance hospital in Zhenjiang from 2014 to 2016. These throat swabs were collected for influenza virus RNA detection and isolation. 13 strains of A(H1N1)pdm09 virus were randomly selected in the epidemic period,then specific primers were designed to sequence the hemagglutinin (HA) and neuraminidase (NA) genes and the genetic characterization of these 13 isolates were analyzed. Results Compared to the vaccine strain A/California/07/2009, the 13 isolated strains shared high nucleic acid sequence similarity in HA and NA genes(97.3%-100.0% and 95.6%-97.5%, respectively), and high amino acid sequence similarity (96.6%-100.0% and 93.8%-96.6%, respectively). The phylogenetic analysis showed that the HA and NA genes of 13 isolated strains were divided into different evolutionary lineages. The molecular characteristics indicated at Sa antigenic site in HA1 domain, 12 isolates had mutations of K173Q,while one had the mutation of K181E. At Ca1 antigenic site in HA1 domain, three isolates had mutations of V183I. Sequence analysis indicated there was no mutation in the receptor binding sites and glycosylation sites. Conclusions Though the HA and NA genes of 13 isolated showed varying degrees of genetic variation compared those of vaccine strain,the antigenicity characteristic remained unchanged. The further monitoring for influenza virus in Zhenjiang is very necessary.