A Ceratocystis Ell. & Halst. species has recently been reported from Acacia mearnsii De Willd. in South Africa showing symptoms of die-back and gummosis. The fungus was tentatively identified as Ceratocystis fimbriata Ell. & Halst. that is a well-known and notorious pathogen of many plants of the world. The fungus from A. mearnsii, however, differs morphologically from authentic C. fimbriata isolates. In this study, isolates from A. mearnsii in South Africa were compared with C. fimbriata isolates from different geographic areas on the basis of morphology and ribosomal RNA (rRNA) sequence data. Morphological comparisons showed that the Ceratocystis isolates from A. mearnsii have light-coloured perithecial bases and divergently arranged ostiolar hyphae compared with entirely black perithecia and convergently arranged ostiolar hyphae of typical C. fimbriata isolates. Comparisons of rDNA confirmed the morphological differences and grouped the South African isolates apart from C. fimbriata originating from other areas. This important pathogenic fungus is consequently described as new.