Amphibians worldwide are threatened by emerging infectious diseases. This includes the recently discovered invasive fungal pathogen Batrachochytrium salamandrivorans (Bsal), which causes chytridiomycosis and is decimating salamander populations in Europe. Continued spread of Bsal is inevitable, and research on host responses and natural immunity is crucial to predict and mitigate the negative consequences to salamanders and cascading impacts to the ecosystems they inhabit. Our understanding of salamander immunity is limited by a lack of functional genomic resources and expertise, which is exacerbated by salamanders’ exceptionally large and complicated genomes. This project will leverage a newly sequenced reference genome and a unique system of two hybridizing Triturus newts with different disease outcomes, to decode the genetic basis of immunity to Bsal. Combining controlled Bsal infections, experimental crosses between resistant and susceptible newts and state-of-the-art genomic techniques and analyses, we will identify the genes associated with Bsal disease resistance in both captive and natural populations. This work will bring major insights into the Bsal-salamander system and amphibian immunity more broadly. The project is expected to have profound long-term implications on captive breeding efforts, and help wildlife managers make informed decisions on population management and disease spread mitigation.