Endemic to southwest of Western Australia (WA), Agonis flexuosa (commonly called peppermint) is a keystone tree species that provides habitat, food, and protection for fauna, particularly the vulnerable Western Ringtail Possum (Pseudocheirus occidentalis). However, this tree species is threatened by diseases caused by pathogens including Phytophthora cinnamomi and Neofusicoccum australe. Commonly, these pathogens cause dieback resulting in tree death. The recent detection of Austropuccinia psidii (myrtle rust) in the Eastern Kimberley adds to the fungal pathogens potentially threatening A. flexuosa in WA. It is uncertain how A. flexuosa will respond to a myrtle rust incursion, given that A. flexuosa has high rust susceptibility but is genetically diverse across its native range. This study aimed to screen A. flexuosa seedlots from different provenances across its native range for resistance to myrtle rust to provide a basis for resistance breeding and species conservation. Phenology studies were undertaken to identify species vulnerability periods for myrtle rust. Further, other fungal pathogens causing diseases on A. flexuosa were investigated with the aim of building a reference library of disease symptoms and existing pathogenic fungi. This study has increased our knowledge of fungal pathogens on A. flexuosa and the information is useful in facilitating disease differentiation from myrtle rust. Importantly, it has also provided new insights into the potential impact should myrtle rust arrive in southwest WA.