Japanese Encephalitis Virus (JEV) is a mosquito-borne flavi virus that causes severe acute viral encephalitis in humans. JEV exists in a zoonotic cycle between mosquitoes and pigs and/or water birds. JEV is a member of the genus Flaviviruses of the Flaviviridae family. The genomic RNA of JEV is a positive-sense, single-stranded RNA. In this study, the primer was studied by the method of segmented design according to the whole sequence (Genebank sequence number M18370) of the genebank JaOArS982 Japanese encephalitis virus strains. The material was gained from Hubei academy of agricultural sciences’ cultured cells. RNA was extracted from the cells and then subjected to RT-PCR, which yielded ten different segments. The complete nucleotide and deduced amino acid sequences of the JEV strain JEV-Yin were determined. The sequenced genome of JEV-Yin was 10,976 nucleotides in length. Sequence comparison of the JEV-Yin polyprotein Open Reading Frame (ORF) with those of 33 other JEV strains revealed that the nucleotide sequence divergence ranged from 0.53% to 25.14%. Sequence analysis of the full-length JEV-Yin E gene sequence with those of 34 other JEV isolates also identified nucleotide divergence, ranging from 0.33% to 22.27%. Phylogenetic analyses indicated that the JEV-Yin strain belonged to genotype III. These results may provide insight into the molecular properties and developing infectious cDNA clone of JEV-Yin strain.