South Africa lies at the meeting point of two ocean systems and experiences significant clines in environmental parameters such as temperature and productivity, which in turn affect the composition and species diversity along its coastline. As such, several biogeographic regions are recognised, which differ in faunal and floral composition. My talk examines the genetic, and more recently, genomic advances that try to unravel the processes that have shaped the patterns of species diversity, particularly in South Africa, with particular emphasis on the past fifteen years. My talk provides an overview of the natural history of South Africa, its marine biogeography and the challenges, constraints and successes of our lab in sequencing species at different spatio-temporal scales and contributing towards highlighting South Africa not only as a region of exception natural interest, but also scientific excellence.