Forests encompass a plethora of biodiversity and house many threatened species. The productivity of the forest is largely dependent on its healthy cover; nonetheless, they are no exemption to biotic and abiotic stresses. Biotic stresses affecting tree productivity are increasing day by day in both natural forests and commercial plantations, among which the important ones are pathogens. The generation and analysis of high-quality genomic data of pathogens is referred to as pathogenomics. The advent of Next-Generation Sequencing (NGS) technologies has revolutionized the field of genomics, and so the pathogenomics. This chapter outlines the wealth of genomic information available on important tree pathogen groups such as fungi, oomycetes, bacteria, viruses, phytoplasma, and phanerogamic parasites, most of which are of pathogens infecting temperate trees. In general, pathogenomics enables understanding of pathogen biology, its variation and evolution. When coupled with host genomics and interactomics, pathogenomics facilitate understanding of the molecular mechanisms underlying disease development that will ultimately provide clues for the sustainable management of diseases the pathogens incite. With its broad arena, pathogenomics will help in tree conservation through identification of the pathogen and development of rapid detection assays for use in quarantine and certification program. Further, it will enable tree breeders to identify candidate genes for deployment in resistance breeding programs or potential targets for gene editing to develop resistance. There exists a huge lacuna in the availability of genome sequences of many important tropical tree pathogens, which are inevitable for their robust detection and management.