Japanese encephalitis (JE ) is the main cause of viral encephalitis in many countries of Asia.The infection is mosquito-borne and caused by the JE virus.The control of JE is based essentially by immunization.JE inactivated vaccine derived from JEV P3 strain (P3-Smb53) have been available in China since decades and have proved effective to control the disease.But the molecular characteristics of the vaccine seed have not been elucidated.In our study,we determined the complete genome sequence and compared with all JEV sequences in Gen-Bank.The results from this study demonstrated that the vaccine seed is 10,976 nucleotides in length and has the same organization as most JEV strains.Even though there are some differences on nucleotide and amino acid sequence among P3-Smb53 and other JEV strains,but on the 12 critical neutralizing epitopes confirmed previously,all the isolates are highly consistent with P3-Smb53.So we conclude that JE inactivated vaccine derived from P3-Smb53 could protect against all the present isolates in nature.