Chronic wasting disease (CWD), a transmissible spongiform encephalopathy of cervids, reached record high prevalence in southeastern Wyoming in 2011 with 57% of harvested mule deer (Odocoileus hemionus) CWD positive. The significance of high CWD prevalence and its impact on free-ranging cervid populations is largely unknown. Previously, CWD susceptibility in mule deer was linked to prion protein (PRNP) genotype at codon 225 with replacement of serine with phenylalanine. Our study investigated the relationship between the population decline and high CWD prevalence as well as the importance of disease-driven natural selection in shaping future population trends. We hypothesized that incorporation of genetic-specific CWD effects in an epidemiologic stochastic spreadsheet model would prevent local extinction of mule deer. Our objectives for this study were to 1) use life-history data collected from radio-collared deer to parameterize models that predicted future population trends within a 100-year period, 2) characterize the impact of CWD on free-ranging mule deer populations, and 3) quantify changes in parameter estimations and their influence on modeled population trends. Our genotype-specific model predicted a 96% reduction in the population with stabilization at a median size of <300 deer by year 100. In contrast, deer were extirpated within 50 years in the absence of genotype-specific incidence and mortality rates. This disparity was due to a 99% decrease and 34% increase in homozygous serine and phenylalanine genotype frequencies, respectively in our genotype-specific model. Our disease-free model predicted stable population growth rates throughout the modeled 100 years. Our results demonstrate the importance of incorporating genetic-specific CWD mortality rates when modeling population trends in free-ranging cervids. Though the negative impacts of CWD are clear despite disease-driven natural selection favoring less susceptible genotypes, persistence of mule deer in our models generates optimism that managers may have time, albeit limited, to find solutions to this epidemic.