The recent global spread of chytridiomycosis across different environments and into multiple species causing mass amphibian decline provides a rare opportunity to look at host pathogen evolution writ large (Skerratt et al 2007, Martel et al 2013). We aimed to identify whether manipulating this evolutionary relationship using the simplest genomic tools such as assisted selection for disease resistance could be used as a management strategy. We found that resistance to chytridiomycosis is evolving. This is good news for the conservation of amphibians still threatened by the disease. We found greater survival in the offspring of long exposed frogs compared with those from naïve frogs as measured in laboratory transmission experiments (Bataille et al 2015). However, selection for greater survival was context specific and variable among populations. We identified MHC resistance markers which can be used to readily identify amphibian populations most suited for assisted selection. Promoting innate immunity artificially may be useful in overcoming the lack of opportunities for natural selection in the wild. In addition, determining whether natural selection is occurring for other mechanisms enabling population persistence such as particular life history traits or behaviours is important. A welcome boost to this approach to managing the major biodiversity diseases chytridiomycosis and white nose syndrome threatening conservation of wildlife is the latest developments in synthetic biology and genetic engineering for human biomedicine.