Puccinia psidii, causal agent of myrtle rust, was discovered in Australia in 2010 and has since become established on a wide range of species within the Myrtaceae. Syzygium luehmannii (Riberry), endemic to the Australian east coast, is becoming an increasingly valuable berry crop. Plants were screened for responses to P. psidii inoculation and specific resistance, in the form of localised necrosis, was determined in 29% of individuals. To understand the molecular basis for this response, mRNA was extracted and sequenced from leaf samples taken pre-inoculation, at 24 and 48 hours post inoculation from four resistant and four susceptible plants. De novo transcriptomes were built for all plants and gene expression profiles compared at each time point. Gene expression profiles were significantly different in resistant versus susceptible phenotypes. Resistant plants significantly up-regulated 185 genes 48 hours after pathogen exposure, while susceptible plants only up-regulated three genes. Most significantly up-regulated in resistant plants were gene homologues coding for transcription factors, receptor-like kinases and enzymes in the secondary metabolite pathway and defence. We identified the presence of putative G-type lectin receptor-like kinase transcripts exclusively in resistant plants and significant differential expression of two transcripts incorporating Toll/interleukin-1, nucleotide binding site and leucine-rich repeat domains.