To obtain a continuous vegetation record of the ancient climate cycles, we studied pollen, spores and micro-charcoal of deep-sea sediments from IODP Site U1479 retrieved from SW of Cape Town. We compared our palynological results of the Pleistocene with previously published results of Pliocene material from the same site. We found that the vegetation of the Greater Cape Floristic Region, in particular Fynbos and Afrotemperate forest, respond to precessional forcing of climate, probably induced by the latitudinal insolation gradient. The micro-charcoal record confirms the importance of fires in the Fynbos vegetation. In addition, lowering of sea-level during the Pleistocene glacials enlarged the terrestrial environment substantially. The expansion of the Palaeo-Agulhas Plain extended the Ericaceae-rich and Asteraceae-rich types of Fynbos, at least on the western part of the plain.