The rust fungus Austropuccinia psidii was recently reported from ornamental Corymbia citriodora and plantations of Eucalyptus in Colombia. It is unknown whether the genotypic diversity of the pathogen in Colombia reflects that of other countries in South America or if unique genotypes occur. Multilocus genotypes (MLG) were determined for collections of A. psidii from four host genera, Corymbia, Eucalyptus, Psidium and Syzygium in Colombia and compared to collections from Australia, Brazil, Indonesia, Paraguay and South Africa. The genotypic diversity of 58 samples on 15 genera of Myrtaceae was determined using seven microsatellite markers. Two lineages of A. psidii were detected among Colombian samples. These included a previously unknown genotype on Psidium guajava, different to those sampled from Brazil, as well as the pandemic biotype, which has spread to Pacific countries such as Australia, Hawaii and Indonesia. This is the first time the pandemic biotype of A. psidii has been found in South America where the rust is believed to be native. These findings raise questions with regard to the origin of the pandemic biotype of A. psidii and emphasise the threat that this biotype poses to forestry.