Abstract: Objective To study the genetic characterization and variation of Japanese encephalitis(JE) virus strains in Guangxi Zhuang Autonomous Region.Methods Totally 12 102 mosquitoes were collected in different areas of Guangxi and Japanese encephalitis virus was isolated by incubating C6/36 and BHK21 cells.E genes of the isolates were sequenced and then homology and phylogenesis were analyzed with bioinformatics software.Results The four Japanese encephalitis viruses isolated belong to genotypeⅠ.Nucleotide similarities of the viruses were 98.3%-99.8%,and the deduced amino acid similarities were 99.4%-99.8%.The most of the nucleotide variations were synonymous mutations.The homologies of the 4 isolates in E gene nucleic acid and amino acid to thsoe of Vietnam Japanese encephalitis strains were up to 99.7%-100%.Comparing the four strains with the standard JE vaccine strain SA14-14-2,the nucleotide sequence homologies were 87.4%-88.0% and amino acid sequence homologies were 96.8%-97.2%,respectively.All the eight sites relavant to the virulence of the virus were variant.There was no variation in the important locations affecting the biological charactetistics of the 4 viruses.Conclusion There is no variation in the important locations affecting the biological charactetistics of the 4 viruses isolated in Guangxi.Compared to the vaccine strain,all the eight sites relavant to the virulence of the virus are variant.