Acacia is a group of shrubs and trees belonging to the subfamily Mimosoideae of the family, the third largest family of flowering plants. They are herbaceous and woody plant distributed mainly in the tropics and subtropics. In recent years most of the Acacia trees were observed to be infected by fungal species causing diseases and gall formation. Acacia species are economically and ecologically important for vegetation, plant products, for browsing and wood. Fungal pathogens infecting plants may lead to great destruction and even extinction of some plant species in the long run, therefore knowing the identity of such fungal pathogens enable us to develop control mechanisms to prevent the further spread of these pathogens thus conserving the Acacia mellifera in its natural habitat. The aim of the study was to isolate and identify the fungal species associated with gall formation on the Acacia mellifera in the western part of Windhoek. Fungal species were isolated from the galls on the infected twigs and grown into pure cultures using Sabouraud Dextrose Agar (SDA) and later on Malt Extract Broth (MEB) as growth media. DNA was extracted from dry mycelia and conserved internal transcribed spacer regions of the fungal species were amplified using the ITS3 and ITS4 primers. DNA amplicons were sequenced and compared to sequences of known organisms in the GenBank using nucleotide BLAST (Basic Local Alignment Search Tool). The BLAST search program revealed the identity of fungal species isolated consistently cultured as an isolate of Phoma glomerata (96 % homology). This organism has previously been reported as common Ascomycota plant pathogen causing dieback disease in most Acacia species. However, further work of testing Koch’s postulates is needed to verify whether Phoma glomerata is directly causing the formation of galls on the Acacia mellifera.