Forest pathogens are a major cause of forest disturbances and they have a significant economic impact on commercial forestry. Genomics is an important technology now available for studies concerning tree health, enabling researchers to better understand pathosystems and potentially to prevent future epidemics from occurring. Comparative genomics at the species level makes possible the identification of unique genomic regions and/or genes that influence the development of pathogens and their ability to cause disease. In addition, population genomics can reveal processes involved in the evolution of pathogens potentially showing how selection and/or environmental adaptation could have driven their emergence. Using these tools, important mechanisms involved in the evolution of pathogens and their hosts can be determined. Practical applications of such knowledge include the formulation of strategies for pathogen detection and surveillance, as well as breeding disease-resistant trees. These new and evolving technologies are set to ensure the long-term sustainability of plantation forestry in the Southern Hemisphere.