Teratosphaeria gauchensis causes a serious canker disease on Eucalyptus spp. In plantations in South Africa and Africa. The pathogen is closely related to, but distinct from T. zuluensis that causes a similar stem canker disease on Eucalyptus. The objective of this study was to use 10 perviously developed polymorphic microsatellite markers to study the population diversity of T. gauchensis, based on collections of the fungus made in Argentina and Uruguay. The alleles were size-analyzed to determine population genetic parameters of the T. gauchensis populations. The results showed that isolates from the two collection sites represent the same population. Overall, the genetic diversity amongst isolates was higher than expected and inconsistent with the nation that the pathogen represents a recent introduction into South America.