Susceptibility to chronic wasting disease (CWD) in cervid species has been associated with polymorphisms in the prion protein gene (PRNP). The single nucleotide polymorphisms (SNPs) were found in the PRNP of the Korean subspecies of Chinese water deer via analyses of the DNA sequences obtained from 34 individual deer. Two SNPs were detected at codons 77 and 100. One SNP at codon 77 encoding Glycine was determined to be a silent mutation but the other SNP detected at codon 100 induced an amino acid change, from Asparagine to Serine. The prion protein (PrP) amino acid sequence of the water deer showed 98.8-99.2% homology with those of American elk, white-tailed deer and mule deer. The PrP of the water deer contained amino acid residues closely related with CWD-susceptibility. This study is the first to describe genetic variations in the PRNP of the Korean subspecies of Chinese water deer.