The high elevated (ca. 1100 m) continental Kalahari Basin (KB) of southern Africa and the linked lower lying (ca. 400 m) Congo Basin (CB) of central Africa preserve in their interiors extensive sedimentary rock sequences and sediments that represent a unique record of the Phanerozoic geodynamic and climatic evolution of sub-Saharan Africa. In this thesis, field observations and new borehole data from the Democratic Republic of Congo (DRC) and Botswana are integrated with new paleontology and geochronology to present a substantially revised stratigraphy for the CB, and south-central Africa in general. This work also introduces a new multiphase model for the subsidence and uplift history of the CB, and improves correlations with the Cape-Karoo Basin (CKB) of South Africa and the Paraná Basin (PB) of south-east Brazil. Four deep boreholes, each between 2 and 4.5 km deep, drilled in the centre of the CB in the 1950’s and 1970’s are re-examined together with the colonial literature (in French) and available seismic data. This stratigraphic and basin analysis is complemented with new U-Pb dates of detrital zircons from core-samples of two of the boreholes (Samba and Dekese), as well as from samples collected during field work in the Kwango region of the south-west DRC. This work, for the first time, constrains the maximum ages and source provenances of the successions in the CB. Following the Pan African orogens (ca. 650-530 Ma), extensive sequences of red beds were deposited by regional paleocurrents to the south. These are now best preserved (1 km thick) along the West Congo, Oubanguides, and Lufilian Belts surrounding the CB. Overlying a hiatus that represents most of the early-Paleozoic, is a 1 to 3 km thick succession of easterly derived glacial, and then continental sequences of the Karoo Supergroup. This succession records the first main episode of subsidence [10-15 m/Ma], interrupted by a phase of uplift that is likely related to far-field intracontinental deformation within Gondwana supercontinent during the Variscan and Cape Fold orogenies (ca. 250-330 Ma) at its peripheries. Detrital zircons from the lower Karoo diamictites are dated at 1.85-2.05 Ga and 1.37- 1.42 Ga, and thus sourced from Paleoproterozoic (Eburnean) and mid-Mesoproterozoic (Kibaran type-I) basement rocks in Uganda and Tanzania. Zircons from all the other successions in the CB date predominantly at 950-1050 Ma and 500-800 Ma. These are derived from sediment recycling of late-Mesoproterozoic (Kibaran type-II) and late- Neoproterozoic (Pan African) sources in the Central African Republic (CAR) and Chad. A distinct unconformity across the Karoo Supergroup in the CB is overlain by 500- 1000 m Jurassic-Cretaceous sequences, here named the Congo Supergroup. During initial rapid subsidence [10-50 m/Ma], late-Jurassic (Kimmeridgian) shallow marine to continental sedimentation attests to a short transgression of proto-Indian Ocean waters into the northern CB (at 160 m above present day sea-level), succeeded by widespread deposition of aeolian dunes that extend from the southern CB to the PB in South America. The youngest zircons from these aeolian sediments in the CB date at 190 Ma and 240-290 Ma, and most likely indicate the influence of extensive silicic volcanic ash derived from the proto-Andes along the south-western margin of Gondwana. Two superimposed mid-Cretaceous (Albian-Cenomanian) lacustrine sequences in the central CB record a succeeding, slower [10-15 m/Ma], phase of basin subsidence during the opening of the South Atlantic (ca. 85-135 Ma). These Cretaceous sequences are in turn truncated by another regional peneplanation surface covered by Cenozoic (Eocene) silcretized sands and alluviums of the Kalahari Group, only 50-250 m thick in the centre of the CB. Southward, on top of the Kalahari Plateau in the central desert region of north-west Botswana, new boreholes intercepted laterally equivalent condensed lacustrine carbonates and calcretes (20-50 m thick) covered by sands. These terrestrial sequences are key archives of late-Mesozoic – Cenozoic paleo-climate changes, yet they remain stratigraphically unresolved. This new analysis of the Phanerozoic continental basins of south-central Africa and their equivalents in South America, opens a fresh continental-scale window into how West Gondwana break-up and concomitant epeirogenic uplifts of Kalahari (>2 km) and Congo (>200 m) are linked to interactions between the lithosphere and mantle geodynamics, and how these processes likely affected global climate changes.