Chrysoporthe cubensis is an important fungal pathogen of Eucalyptus species worldwide. The fungus is also known on many other hosts, all residing in the order Myrtales. Previous studies have suggested that Chr. Cubensis might be native to South America and southeast Asia and that it has been introduced into Africa. Recently, surveys have been conducted in eastern and southern Africa to assess the distribution of Chrysoporthe spp. in this region. Chr. Cubensis was found on Eucalyptus spp. in Kenya, Malawi and Mozambique. The aim of the study reported here was to determine the genetic diversity of Chr. Cubensis populations from these countries. Population diversity studies were conducted using five pairs of microsatellite markers previously developed for Chr. cubensis. Results show that there is a very low genetic diversity within the populations of Chr. Cubensis from Kenya, Malawi and Mozambique, implying that the fungus was probably recently introduced in these countries. Based on phylogenetic analyses, the origin of East African Chr. Cubensis is most likely Asia.