Over the past decade, Puccinia psidii, which causes rust on species of Myrtaceae, has spread rapidly to new areas and is now widespread. Quarantine has done little to prevent its movement through America, the Pacific, Africa, and in this report, SouthEast Asia. Puccinia psidii is reported for the first time from Indonesia on two genera of Myrtaceae, namely Eucalyptus and Melaleuca. The identity was confirmed by morphology, a molecular barcode comparison to an epitype specimen, and with a molecular phylogenetic approach. Comparison of seven microsatellite markers revealed that the genotype of the rust in Indonesia is the same as that found in Australia. The potential impacts of P. psidii in South-East Asia to the natural environment and plantation forestry are discussed in light of this first report from the region.