Abstract Adansonia gregorii (baobab) is an iconic tree species occurring in the north-west of Australia. Dying baobabs, A. digitata, have been reported from southern Africa and as A. gregorii is closely related to A. digitata, surveys were conducted to assess the health of the Australian baobab. The endophytic microflora of A. gregorii and surrounding tree species was sampled and the ability of these endophytes to cause disease in A. gregorii was determined. Endophytes were isolated from asymptomatic baobabs across 24 sites in the Kimberley region, north-west Australia. Material was also taken from surrounding native tree species at three sites. Material was also collected from asymptomatic and dying Adansonia species in the George Brown Darwin Botanic Gardens and from a dying baobab in a nursery in Broome. Endophytic fungi isolated from these samples were identified using morphological and molecular methods. Eleven botryosphaeriaceous species were identified along with 18 other non-botryosphaeriaceous species; Lasiodiplodia theobromae was the most common species. The pathogenicity of the botryosphaeriaceous species to baobabs was determined by inoculating the taproot of seedlings and stems of young baobab trees. Lasiodiplodia theobromae was confirmed as a potentially significant pathogen of baobabs.