The marine origin of black shales in the context of the Permian postglacial development of the Karoo Basin, South Africa, is subject of an ongoing controversial discussion. Here, we present and discuss palynological and sedimentological data providing evidence of a transgressive event during the early Guadalupian. Palynofacies assemblages of the black shales of the southern basin include marine phytoplankton that exhibit peak abundance within the Whitehill shales and which also occur within siltstones and glauconitic sandstones on top of the No. 5 coal seam of the north-eastern basin. Palynostratigraphic control makes this marine signal a powerful tool for cross-basin correlation. Moreover, palynofades analysis demonstrates a facies transition from terrestrial lacustrine and fluvio-deltaic in the northeast to deep marine in the south-western parts of the basin.