Geological maps are a powerful but underutilized tool for constraining geodynamic processes and models. Unraveling the Cenozoic elevation history of Africa and distinguishing between competing uplift and subsidence scenarios is of considerable interest to constrain the dynamic processes in the mantle beneath the continent. Here, we explore continental-scale geological maps, and map temporal and spatial patterns of geological contacts, assuming that interregional-scale unconformable contacts (hiatus surfaces) on geological maps yield proxy records of paleotopography and vertical motion. We found that significant differences in the spatial extents of interregional-scale hiatus surfaces exist across Africa at the timescale of geologic series. A significant expansion of total unconformable area at the base of the Miocene strongly suggests that the Oligocene was a period of uplift in most of Africa. In southern Africa there is a complete absence of marine sediments in both the Oligocene and Pleistocene. This pattern suggests that southernmost Africa reached a high elevation in the Oligocene, subsided in the Miocene–Pliocene, and has been high again since the latest Pliocene or Pleistocene. Our hiatus mapping results support a dynamic origin of Africa’s topography. In particular, they point to elevation changes at the timescale of geologic series (ten to a few tens of millions of years), which is considerably smaller than the mantle transit time. The timescale for elevation changes in Africa is, thus, comparable with the rapid spreading in the South Atlantic, which have been geodynamically linked to African elevation changes through pressure-driven upper mantle flow.

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