Acacia koa and A. heterophylla are commonly occurring native trees on the Hawaiian Islands and La Réunion, respectively. A recent phylogenetic study suggested that A. heterophylla renders A. koa paraphyletic, and that the former likely arose from the Hawaiian Islands around 1.4 million years ago. An intriguing question is whether their microbiota is similar, although they occur naturally in two very distant geographical locations. In this study, we compared the fungi in the Botryosphaeriaceae isolated from natural populations of A. koa and A. heterophylla. These fungi were chosen because they commonly occur on woody plants and some are important pathogens. They are also known to have been moved globally on asymptomatic plant materials. Isolates were identified based on comparisons of DNA sequence data for the rDNA-ITS, TEF1-α and β-tubulin loci. Ten Botryosphaeriaceae species were identified, of which four species were specific to A. koa from the Hawaiian Islands and five to A. heterophylla in La Réunion. Only one species, Neofusicoccum parvum, which is known to have a wide global distribution, was common to both hosts. The overall results of this study suggest that although A. koa and A. heterophylla share a recent evolutionary history, they have established independent microbiota, at least in terms of the Botryosphaeriaceae.