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South Africa has a limited number of peatlands and most of them are relatively small compared to those in cooler temperate regions in the northern hemisphere. We gathered 40 basal peat samples representative of South Africa's peatlands to explore their development during the Late Pleistocene and Holocene. Depth profiles of nine of them were also investigated using radiocarbon dating, which yielded information on past environmental changes affecting South African peatlands. The data showed three peaks in the frequency of peatland initiation, which are consistent with available climatic and sea level fluctuation data: one after the Last Glacial Maximum (LGM) and two during the Mid to Late Holocene. Inland peatlands in mountain valleys showed optimal growing conditions during the glacial-interglacial transition, continuing until the Early-Holocene. This is due to the switch to the wet and warm interglacial climate. In contrast, coastal peatlands showed optimal initiation conditions over two phases during the Holocene, which is consistent with sea level rise peaks that led to optimal moist conditions occurring ca. 6,000-3,000 and 1,000 years ago. Sea level rise reduced groundwater drainage, which led to a rise in the primary groundwater table. However, data from some of the coastal peatlands indicate independence from the sea level fluctuation, and that they are rather controlled by climatic conditions and their local hydrogeomorphic setting, e.g. perched groundwater aquifers. Some peatland complexes show a pattern of phased initiation with peat initiation consistent with altitude difference, which could be due to a positive feedback of blocking caused by peat accumulation in lower reaches, reducing groundwater drainage to the sea.