According to the published E genes sequence of JEV in GenBank, two pairs of PCR primers were designed. E genes were amplified from JEV-SD001 strain. Then the PCR products were cloned into pMD-18 Easy Vector, and the recombinant plasmids were obtained. The sequence of the cloned PCR products were analyzed with other JEV isolates in GenBank. The results indicated that the homology of their nucleotide sequence was over 97.2%, and it shared over 96.8% of amino acid homology with other JEV isolates. JEV-SD001 belonged to Japanese encephalitis virus genotype Ⅲ, E protein of isolates showed some differences as compared with vaccine strains.