Prion disease has displayed large infection host ranges among several species; however, dogs have not been reported to be infected and are considered prion disease-resistant animals. Case-controlled studies in several species, including humans and cattle, indicated a potent association of prion protein gene () polymorphisms in the progression of prion disease. Thus, because of the proximal location and similar structure of the gene among the prion gene family, the protein gene () was noted as a novel candidate gene that contributes to prion disease susceptibility. Several case-controlled studies have confirmed the relationship of the gene with prion disease vulnerability, and strong genetic linkage disequilibrium blocks were identified in prion-susceptible species between the and genes. However, to date, polymorphisms of the dog gene have not been reported, and the genetic linkage between the and genes has not been examined thus far. Here, we first investigated dog polymorphisms in 207 dog DNA samples using direct DNA sequencing. A total of four novel single nucleotide polymorphisms (SNPs), including one nonsynonymous SNP (c.149G>A, R50H), were identified in this study. We also found two major haplotypes among the four novel SNPs. In addition, we compared the genotype and allele frequencies of the c.149G>A (R50H) SNP and found significantly different distributions among eight dog breeds. Furthermore, we annotated the c.149G>A (R50H) SNP of the dog gene using tools, PolyPhen-2, PROVEAN, and PANTHER. Finally, we examined linkage disequilibrium between the and genes in dogs. Interestingly, we did not find a strong genetic linkage between these two genes. To the best of our knowledge, this was the first genetic study of the gene in a prion disease-resistant animal, a dog.