Amino acid polymorphisms of the prion protein (PrP) gene (PRNP), particularly those occurring at codons 136, 154, and 171 have a significant influence on scrapie pathogenesis in many sheep breeds. We isolated blood samples from 222 sheep representing the eight main local sheep breeds in the Xinjiang Autonomous Region, the territory with the most abundant local sheep breeds in China, to identify the PRNP polymorphisms and to determine whether these breeds were at risk for developing scrapie. A new PRNP polymorphism encoding either glycine (G) or arginine (R) at codon 85 as well as eight previously reported polymorphisms at codons 101, 112, 127, 141, 146, 154, 171, and 189 in other sheep breeds were detected. Interestingly, the alanine (A)/V polymorphism at codon 136 was not observed in this study, all sheep being homozygous for A at this position. While the previously identified polymorphism of argine (R) or histidine (H) at codon 154 was detected, the H polymorphism was rare (2.25%). Four polymorphisms at codon 171 encoding glutamine (Q), R, H, or lysine (K) were detected. The predominant ARQ allele occurred at a high frequency of 77.48%, suggesting an increased risk of scrapie in Xinjiang Autonomous Region.