Fungal pathogens challenge the integrity of natural environments while threatening global food security and forestry industries. The occurrence of new and emerging plant fungal infections is on the rise, particularly in the context of land use change, but has gone largely unnoticed because of inadequate detection methods. To effectively address existing knowledge gaps relating to the emergence of fungal pathogens associated with land use change, an interdisciplinary approach to research is required. Such research should bridge gaps between the fundamental studies of taxonomy, ecology and distribution modelling, as well as the applied sciences related to land use management, agricultural production and plantation forests. Without a cohesive plan linking these disciplines and sectors, it would be impossible to fully understand how fungal pathogens enter an ecosystem and how to mitigate the resultant damage in the future. There is a need to develop sustainable plant protection strategies, requiring fresh insight into the biology and evolution of the corresponding pathogens. Currently, there are very few early warning systems or mechanisms for predicting a fungal pathogen outbreak in agricultural or tree-based systems; it is thus imperative that, as a first step, we generate a fundamental understanding of how these outbreaks occur. In the following chapter, we aim to discuss these issues and make suggestions on how to better research and manage land use change and the related fungal pathogens. We suggest that in order to better predict how or when an outbreak might occur, scientists should begin by studying the natural reservoirs of fungal pathogens before determining stable states in fungal communities and associated communities of fungal pathogens. Next, it is important to determine how these communities change as they are exposed to external pressures, such as land use conversion. Finally, it is crucial to better understand what environmental triggers lead to increased pathogenicity in fungal pathogens and related shifts in life mode strategies, causing beneficial fungi to shift into a pathogenic mode.