Biodiversity, the variety of animal and plant species, has important economic and cultural values for mankind; yet species are going extinct at a dramatic rate worldwide. An important cause is the emergence of new diseases, often facilitated by human activities. Reducing their impact can help preserve biodiversity, but is difficult because we often know little about the diseases, the affected species, and the possible response actions. Management must be adaptive, recognising limited knowledge and incorporating new information provided by research. Our project aims to develop a protocol for adaptive management of wildlife diseases, testing it on a recently discovered threat. In 2014, a new deadly species of fungus was found to be causing the disappearance of salamanders in Belgium and the Netherlands. It may have been released accidentally with pets and is rapidly expanding. We will map the risk of the disease spreading and identify possible response actions. We will then use mathematics to identify which little-known aspects of the disease are most important to clarify, how such information could be collected through field monitoring or laboratory experiments and how response strategies could adapt to new knowledge. We will compare response strategies in the Low Countries, where the disease is currently raging, and in Spain and Italy, where its arrival could severely affect rare local species. Our protocol will also inform future management of wildlife diseases worldwide.