The Greater Cape Floristic Region of South Africa is a relatively small area found in the south-western corner of the African continent. It is characterised by a Mediterranean-type climate and harbours an incredible floral diversity with almost 11,500 species of plants, of which more than three-quarters are found nowhere else in the world. The floristic composition of the region is very distinctive with families not dominant in other floras, such as Iridaceae, Aizoaceae, Ericaceae, Proteaceae and Restionaceae. In addition, small-leaved, sclerophyllous low shrubs and geophytes are by far the predominant growth forms with a low proportion of tree and annual species present. Understandably, this flora has attracted a lot of interest, and many have pondered what environmental and ecological factors could be responsible for its richness and uniqueness and the resulting biodiversity patterns observed today. In this chapter, the current state of knowledge of large-scale evolutionary patterns, investigated using phylogenetic diversity metrics, within the Cape region are reviewed. As well as published works, we report on ongoing studies examining biodiversity patterns using phylogenetic diversity, phylogenetic endemism and phylobetadiversity, both in plants and animals. We also review how these phylogeny-based approaches have been used to address applied questions (e.g. biodiversity surrogates, phytogeographical delimitations).