Myrtle rust is a fungal disease that is spreading worldwide, threatening the biodiversity of Myrtaceae plants such as Syzygium, Eucalyptus and Melaluca. These plants are key foundation species for wildlife, have high agricultural value and are iconic in Australian culture. Many plants will have poor or no defence against this highly infectious, mutating and rapidly spreading fungus. The extent of post-transcriptional modifications is largely unexplored in pathogen-plant interactions but may play key roles in transcript function and stability during pathogen attacks. We investigated Austropuccinia psidii (myrtle rust) and Syzygium jambos (rose apple) before and after myrtle rust infection, by direct RNA sequencing with the Oxford Nanopore Technology MinION platform. Direct RNA sequencing revealed differential gene expression, alternative splicing and what dynamic, reversible modifications are made to the RNA, such as methylation. We identified key transcriptional genes and pathways activated during myrtle rust infection, investigated the roles of transcript diversity from alternative splicing in the response to infection and identify potential roles of differential RNA modifications during infection and defence. Our research goal is to increase the understanding of pathogen-plant interactions and determine if alternative splicing and RNA modifications play signification roles in infection or plant immunity.