Large numbers of Acacia cyclops trees are dying along the coastal plains of the Eastern and Western Cape Provinces of South Africa. The cause of the deaths has been attributed to a root and butt rot disease caused by the basidiomycete fungus Pseudolagarobasidium acaciicola. However, many signs (e.g. basidiomes) and symptoms reminiscent of Ganoderma root-rot are commonly associated with the dying trees. In this study, isolates collected from basidiomes resembling species of Ganoderma, as well as from root and butt samples from diseased A. cyclops trees were subjected to DNA sequencing and morphological studies to facilitate their identification. Multi-locus phylogenetic analyses and morphological characterisation revealed that three species of Ganoderma are associated with dying A. cyclops trees. These included G. destructans, a recently described species causing root-rot on trees elsewhere in South Africa. The remaining two were novel species, one of which is described here as G. dunense. The novel species is distinguished by its mucronate basidiomes, laccate shiny pileus surface, duplex context and ovoid basidiospores. Only an immature specimen was available for the second species and a name was consequently not provided for it. Interestingly, only a single isolate representing P. acaciicola was recovered in this study, suggesting that further investigations are needed to ascertain the role of each of the four basidiomycetous root-rot fungi in the death of A. cyclops trees.