During a survey of Eucalyptus diseases in Ethiopia, a serious stem canker disease was discovered on E. camaldulensis trees at several localities in the south and south-western parts of the country. The disease was characterised by the presence of discrete necrotic lesions, stem cankers, cracking of stems, production of kino pockets in the wood, as well as malformation of stems. These symptoms are similar to those caused by Coniothyrium zuluense in South Africa. This study identified the causal agent of the disease in Ethiopia by sequencing the ITS regions of the rRNA operon for a representative set of isolates. Sequences for the Ethiopian isolates were compared with those from authenticated isolates collected in South Africa, Thailand and Mexico, as well as with Coniothyrium-like isolates collected from diseased Eucalyptus trees in Uganda. Pathogenicity trials were also conducted in the greenhouse to determine the virulence of Ethiopian isolates. Based on comparisons of sequence data, the pathogen causing the stem canker disease in Ethiopia was identified as C. zuluense. Isolates from Ethiopia, however, formed their own sub-clade, reflecting geographic isolation of the pathogen. Results, furthermore, also show that C. zuluense does not reside with other Coniothyrium spp., but rather within the genus Mycosphaerella. Small lesions were obtained from inoculated Eucalyptus trees, proving that the fungus is the cause of disease in Ethiopia. This study represents the first confirmed report of C. zuluense and the disease caused by it in Ethiopia and Uganda. It also shows that C. zuluense is closely related to species of Mycosphaerella and not other Coniothyrium spp. and that it will require a name change in future.