The chytrid fungus Batrachochytrium dendrobatidis (Bd) has fuelled global amphibian declines. The Andes represent an epicentre of Bd-driven extinctions. However, the long-term coexistence of susceptible, yet surviving host populations with Bd remains enigmatic. I propose coevolution as the main driver of coexistence, leading to reduced pathogen virulence. My project integrates phylogeography, phenotypic diversity, and host-pathogen metatranscriptomics to elucidate the mechanisms mediating coexistence from a pathogen view. The project focuses on Bd’s lineage diversity across a pan-Andean landscape, leveraging recent advancements in sequencing and host-pathogen profiling. I predict that Bd strains from areas with amphibian population survival evolved towards reduced virulence compared to strains from extinct populations. Work Package 1 (WP 1) reconstructs Bd’s invasion biogeography using genomic data. WP 2 unravels phenotypic diversity, thermal niches and gene expression of distinct contemporary Andean Bd lineages and WP 3 examines gene expression in a coevolved host to endemic and hypervirulent Bd lineages, identifying key immune and virulence pathways. This research represents the first fine-scale integration of genomic, phenotypic, environmental and transcriptomic data on Bd at a landscape level, providing novel insights into pathogen evolution and host coexistence. The findings will inform conservation strategies and are crucial to understand and mitigate fungal pathogens.