Rocks of the Late Carboniferous to Early Jurassic aged Karoo Supergroup of South Africa preserve a sedimentary succession, deposited in a retro-arc foreland setting. This succession documents environmental change from glacial-marine, through full marine to continental fluvial and aeolian environments, culminating in rift associated continental flood basalt extrusions. The Karoo Basin is internationally renowned for its wealth of fossil tetrapods, enabling the establishment of a reliable and useful biostratigraphic framework which has international applicability for correlation of Permian-Triassic tetrapod-bearing continental deposits. The transition from marine to continental deposition in the Karoo has been the subject of much recent research, particularly in regard to the position of the Ecca-Beaufort contact. Our study indicates for the first time that in the south-eastern part of the basin, as for the rest of the basin, this transition comprises three separate facies associations deposited respectively in the prodelta, subaqueous delta plain and subaerial delta plain environments. The Tapinocephalus Assemblage Zone is the lowermost vertebrate biozone in the Koonap Formation indicating that the Ecca-Beaufort boundary is diachronous in the southern part of the basin, younging towards the east. This supports the easterly to northeasterly prograding shoreline model previously proposed for the Ecca-Beaufort transition and provides new insight on the distribution of the earliest land-living vertebrates in the south-eastern Karoo Basin.