Chronic wasting disease (CWD) is increasingly prevalent in multiple wild mule (Odocoileus hemionus) and white-tailed deer (O. virginianus) herds in North America. CWD was first found in Canadian wild mule deer in Saskatchewan in 2000 and has since spread into the neighboring province of Alberta. The infectious agent for CWD is a misfolded prion protein encoded by the PRNP gene. Previous studies revealed association between PRNP genotype and susceptibility to CWD in both mule and white-tailed deer in other regions. To investigate this link in Canadian populations, PRNP gene sequence was examined in 166 CWD- and 83 CWD+ mule deer, and 197 CWD- and 30 CWD+ white-tailed deer from Saskatchewan and Alberta. Two variable sites were found in mule deer, and 15 in white-tailed deer. In both species PRNP genotype was associated with CWD status. Mule deer possessing at least one copy of the common allele at codon 20 were less likely to test positive for CWD than expected, given the frequency of this allele in the population. A variant at codon 96 in white-tailed deer was also linked with reduced incidence of CWD. A greater knowledge of the genetic sources of heterogeneity in CWD susceptibility may improve our understanding of the mechanisms underlying the CWD epidemic in western Canada.