Fungi cause severe crop losses and threaten food security worldwide. The soil-borne fungal pathogen Verticillium dahliae causes vascular wilt disease on hundreds of plant species, and disease control is challenging because resistance in plants is rare. Moreover, V. dahliae has a flexible genome allowing it to escape host immunity and maintain aggressiveness. Through comparative population genomics we try to unravel mechanisms to establish genomic diversity that is essential for adaptive genome co-evolution during the continued arms race with host plants. These analyses have revealed lineage-specific regions within V. dahliae genomes that are important for virulence. Interestingly, these regions are enriched for in planta-expressed effector genes encoding secreted proteins that enable host colonization. Some of these effectors enable host specificity.