Emerging diseases often originate from host shifts of introduced pests or pathogens. Genetic resistance of the host to such diseases might be limited or absent due to the lack of coevolutionary history. We review six examples of major disease outbreaks on native tree species caused by different introduced pests and pathogens that led to large ecological and economical losses. In all six cases, high tree mortality was observed in natural populations with some surviving individuals exhibiting varying levels of genetic resistance. The abundance and distribution of resistant individuals and the heritability of resistance traits varies substantially among the cases. While chestnut blight wilt combined with ink disease has virtually eliminated mature Castanea dentata trees from North America, other severe emerging diseases, such as the ash dieback, have left many surviving trees and genetic variation in resistance to such diseases has been documented. We argue that the evolutionary potential of tree species to respond to new emerging diseases should not be underestimated. However, the risk of increased levels of inbreeding and loss of genetic diversity caused by low population sizes is a major concern. Maintenance of broad genetic diversity is an important issue in conservation and forestry management. We expect that future research targeting the genetic background of biotic resistance towards emerging diseases and the role of endophytic communities in protecting trees will facilitate the informed and science-based guidance required to manage and maintain forests with high resilience. International cooperation on limiting disease spread and the provision of early invasive pest or pathogen detection systems are essential.