Coniothyrium canker caused by the fungal pathogen Teratosphaeria (= Coniothyrium) zuluensis is one of the most important diseases affecting plantation-grown Eucalyptus trees. Little is known regarding the pathogen and this study consequently considers the genetic diversity and population structure of T. zuluensis. Eleven microsatellites markers, of which six were developed in this study, were used to analyse two temporally separated populations of T. zuluensis from South Africa, one population from Malawi and one population from China. Results showed that the populations of T. zuluensis have a moderate to high diversity and that clonal reproduction is predominant. There was also evidence that the genetic diversity of the pathogen in South Africa has increased over time. Comparison of T. zuluensis populations from South Africa, Malawi and China suggest that South Africa is most probably not the centre of origin of the pathogen as has previously been suggested.