Some species of the Botryosphaeriaceae are capable of infecting a broad range of host plants. We studied the species diversity of Botryosphaeriaceae associated with marula (Sclerocarya birrea subsp. caffra, Anacardiaceae) trees in South Africa over two seasons, as well as species common to both S. birrea and adjacent mango (Mangifera indica, Anacardiaceae) trees in a subset of sites. Gene flow amongst populations of Botryosphaeriaceae shared on these tree species was tested using microsatellite markers. Twelve species were identified from S. birrea and eleven species were found on M. indica trees. From isolations done in 2006, the dominant species on S. birrea was Neofusicoccum vitifusiforme, while N. parvum was the dominant species isolated from M. indica. Neofusicoccum parvum was dominant in isolations from both hosts in 2012. Isolates of Botryosphaeria fabicerciana, Lasiodiplodia mahajangana, L. pseudotheobromae, L. theobromae, N. mediterraneum, and N. umdonicola were also collected from both hosts. Population genetic analyses on isolates of N. parvum suggested that three populations were present, each comprising isolates from both hosts. There was significant gene flow between N. parvum populations on these hosts. This ability to infect multiple hosts and to migrate amongst them facilitates the establishment and spread of species and genotypes of the Botryosphaeriaceae, such as N. parvum, in new areas.