Fungi are a remarkably diverse kingdom with an estimated 1.5 million species. They form intimate interactions with a broad array of other organisms, including mutualisms, symbioses and as decomposers. Yet their essential role supporting life on earth has often been matched by their ability to cause devastating diseases in humans, animals and plants. Given that emerging fungal infectious diseases pose serious threats to public and wildlife health, food security, and ecosystem stability, understanding fungal evolution and adaptations to biotic and abiotic factors has never been more urgent. We argue that an in-depth study, combining population and comparative genomics, of one fungal clade containing pathogenic and non-pathogenic species will be critical to better understand the genomic determinants of fungal adaptation. Indeed, these two complementary approaches extract information on different timeframes and as a result draw a more complete and accurate picture of events and processes acting across fungal genomes. We propose to investigate the fungal genus Pseudogymnoascus, comprising one pathogenic species infecting bats (Pd) and more than 45 closely related species not pathogenic to bats. We will (1) characterise the Pd pangenome architecture, content and variability, and test if the species follows the two-speed genome model, (2) identify Pd genomic regions that are involved in local adaptation generally and those that are associated with key biotic and abiotic adaptations specifically, (3) Identify genomic characteristics differentiating pathogenic and non-pathogenic species, and (4) extent our work to characterise the relationship between life-history traits, genome properties and evolutionary processes across Ascomycota.