Introduced species and infectious diseases both independently pose challenges for the preservation of existing biodiversity. However, native species or disease hosts are by no means ‘unarmed’ when faced with novel environmental challenges, provided that adequate adaptive genetic variation exists to mount effective evolutionary responses. In this study, we examined the consequences of the recently introduced parasite and causative agent of whirling disease (Myxobolus cerebralis) in a wild rainbow trout (Oncorhynchus mykiss) population from Harrison Lake, Montana (USA). Consistent with the parasite’s age-specific effects, juvenile rainbow trout recruitment into Harrison Lake was substantially reduced following parasite detection in 1995. However, experimental data suggest that natural selection has rapidly reduced whirling disease susceptibility within the population over time. The rapid observed temporal change in resistance patterns argues that the standing genetic variation for parasite resistance facilitated this process. Our findings ultimately underscore the importance of preserving genetic diversity to ensure that species of economic importance or of conservation concern have maximal chances for persistence in future changing environments.