The characterization of the 5 Korean isolates (K96P10, K94P05, K91P55, K87P39, and K82P01) of Japanese encephalitis virus (JEV) was compared with JE virus prototype Nakayama-NIH (NKY-NIH) using prM/M and envelope gene sequences of the JEV genome and phylogenetic analysis. The antigenic analysis of these viruses were done by the cross-hamagglutination inhibition (HI) test using polyclonal antibodies against Korean isolates and NKY-NIH. The sequence homology of the Korean isolates and NKY-NIH ranged between 87.4 % - 95.6 % at the nucleotide level and between 98.2 % - 97.2 % at the amino acid level over the E nucleotides compared. Alignment of E protein amino acid sequences revealed that residue positions E89, E129, E221, E244, E327, E366, E459, and E477 characterized the Korean strains. According to phylogenetic analysis bases on the E nucleotide, there are at least 2 genetic types of JEV existing in Korea and Korean strains were distinct from NKY-NIH. However, the cross HI test results of all the Korean isolates were serologically no different from NKY-NIH strain.