Resource managers are often presented with dilemmas that require immediate action to avoid species extinction, but that also ensure species long-term persistence. These objectives may conflict with one another, resulting in new threats as initial threats are ameliorated. Such threat evolution is a common pattern in the long history of efforts to conserve endemic trout (Salmonidae) populations in western North America. Early conservation strategies were often successful in reducing initial threats of hybridization with non-native trout, but were also responsible for producing new threats such as inbreeding, genetic drift, and, more generally, reductions in heterozygosity. In such situations, the objective of reducing or minimizing the threat of extinction remains the same, but the causes of decline change in direct response to the implemented strategy. This aspect of species recovery is not often recognized in initial efforts to protect a species from extinction. Here, we present the case of the threatened Little Kern golden trout (O. mykiss whitei), as an example of threat evolution. Its conservation management history is well documented, as are feedbacks between direct conservation actions and emerging present-day threats. Management of this and similarly imperiled species must take into account evolving threats, if long-term persistence is to occur.