Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South Africa's chondrichthyans are threatened with extinction. South Africa's commercial shark fisheries have increased over the last decade and there is a need to ensure sustainable utilisation and conservation of this fisheries resource. Here, we give an overview of the molecular techniques that are used to assist in the identification of species, cryptic speciation and possible interspecific hybridisation, as well as the assessment of population structure and reproductive behaviour of endemic and commercially important chondrichthyan species of southern Africa. We discuss the potential application of these techniques for management and conservation of several species affected by South African fisheries. Acquiring baseline barcode data of all chondrichthyans in southern African waters and assessing the population structure of exploited species on a local and greater regional scale are recommended as research priorities. Future prospects should also include high-throughput molecular marker development and investigation of intraspecies functional variation using next generation sequencing technology.