The Botryosphaeriaceae (Ascomycetes), with more than 2000 species (http://www.indexfungorum.com), represents one of most widely distributed groups of fungal plant pathogens. These species are known to infect both economically important crops and native plants. In this study species of the Botryosphaeriaceae associated with native woody hosts in South Africa and Western Australia were investigated. Based on ITS rDNA sequence comparisons, combined with phenotypic characters and PCR-RFLP analyses, eight species were identified on native Syzygium cordatum in South Africa. These included Neofusicoccum parvum, N. ribis, N. luteum, N. australe, N. mangiferae, Botryosphaeria dothidea, Lasiodiplodia gonubiensis and L. theobromae. Three additional cryptic species were identified in the N. parvum / N. ribis complex from S. cordatum using five gene genealogies and the genealogical concordance phylogenetic species recognition (GCPSR). These are the first species of the Botryosphaeriaceae described using fixed single nucleotide polymorphisms (SNPs) as a defining character, and are described as N. cordaticola, N. kwambonambiense and N. umdonicola. The analysis of microsatellite marker data supported the distinction of these species. These data were also used to characterise the distribution of the latter three species and N. parvum on S. cordatum. Finding the same haplotypes of N. parvum on S. cordatum and closely related, planted Eucalyptus indicates movement of this pathogen between these hosts. Since all of the species recognised from S. cordatum were pathogenic to Eucalyptus, and the newly described species were more virulent than N. parvum and N. ribis on S. cordatum, their movement between hosts can pose a serious treat to both native and non-native plants. From Western Australia, molecular sequence data and morphological analyses revealed seven new species of the Botryosphaeriaceae from baobab and other native trees. These included Dothiorella longicollis, Fusicoccum ramosum, Lasiodiplodia margaritacea, Neoscytalidium novaehollandiae, Pseudofusicoccum adansoniae, P. ardesiacum and P. kimberleyense. In the literature review, which also considers work done in this thesis, the influence of molecular tools on the taxonomy of the Botryosphaeriaceae during the last decade, with a particular focus on cryptic species recognition, is considered. This study clearly showed that a polyphasic approach in species identification, as well as investigation of less well studied native flora, will reveal numerous new and cryptic species in the Botrysphaeriaceae and improve our knowledge of this group of important plant pathogens in the future.