Myrtle rust is a plant pandemic caused by the fungus Austropuccinia psidii. It impacts certain species in the iconic Myrtaceae plant family which includes eucalypts and tea-trees. This study predicts myrtle rust will cause a plant extinction event of unprecedented magnitude. We conducted extensive field surveys of Australian rainforest to determine which locations, habitats and species have been impacted by the fungus since its detection in this country in 2010, surveying 145 Myrtaceae tree species, from 1900 plant populations across 935 rainforest sites. All field survey information has been entered into a myrtle rust database to evaluate the spread of the disease over time and across the landscape. The results predict the imminent extinction of 16 rainforest tree species in the wild within a generation, with another 20 species also at risk of extinction. Myrtle rust retards plant growth and prevents reproduction on severely affected plants. We have been monitoring populations of the native guava (Rhodomyrtus psidioides) and found a severe decline in population number and health: this species is now nearly extinct in the wild as a result of myrtle rust. Protecting populations in the wild with targeted use of fungicide, translocation into new locations and breeding of rust-resistant individuals will be important conservation strategies for the Myrtaceae plant family.