Objective:The gene sequence of Hantavirus isolated strains during 2009 and 2013 was analyzed at molecular level to provide evidence for the prevention and control of this disease. Methods:The serum of patients with acute hemorrhagic fever with renal syndrome(HFRS)and rat lung specimens were collected from 2009 to 2013. Hantavirus IgM and IgG antibody in serum samples and antigen in mouse lung samples were detected using colloidal gold and IFA assay,respectively. With VERO E6 cell line,Hantavirus was isolated,then analyzed using RT-PCR assays,and genome was sequenced using high-throughput sequencing technology. Finally,sequence alignment and phylogenetic analysis were accomplished with MEGA6.0 software. Results:With the closest genetic distance,isolated 11 virus isolates and Shanxi LR1,Sichuan isolates s85-46 and Hantavirus strain 76-118 prototype were all classified as Hantaan (HTN)virus. In addition,strains isolated in Jiangsu 2002 (A9,HTN type)and strains in Zhejiang and Anhui on different evolutionary branches,indicated a larger genetic distance. Conclusion:Both Hantavirus predominant strains switchover and host transfer have happened in Jiangsu. Surveillance should be strengthened to guarantee the efficacy of the vaccine.