We determined the nucleotide and deduced amino acid sequences of the complete envelope (E) protein gene of the five tick-borne encephalitis virus (TBEV) strains KrM 93, KrM 213, KrM 215, KrM 216, and KrM 219, isolated from wild rodents in South Korea. We analyzed genetic variability within the isolates and compared them with 13 other TBEV strains. The complete E protein genes were amplified by reverse transcription polymerase chain reaction (RT-PCR), cloned into pGEM-T vectors, and sequenced. The five isolates were similar to the Western subtype in nucleotide and deduced amino acid sequences (97%-99% identity) and by phylogenetic analysis. The deduced amino acid alignments had 13 unique amino acids, as in the Western subtypes. Among the signature amino acids, those at positions 206 and 317 were unique to each subtype. We were also able to identify amino acid substitutions in each of the three domains when comparing the 5 Korean isolates with the 13 other TBEV strains. Thus, we confirmed that the 5 Korean isolates belong to the Western subtype. These data will provide useful information for the development of an effective recombinant vaccine.