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Abstract The southern African plate underwent significant stresses since the Permian attributed to orogenesis and to mantle upwelling during Gondwana break-up. Rift basins developed over ancient basement structures during Early Permian and since the Cretaceous along the passive margin. We investigated the exhumation history of Precambrian basement rocks of the Karoo rift flanks of NW Mozambique using apatite fission tracks (AFT). Twenty seven samples were collected from the northern, center and southern areas surrounding the E-W and NW-SE-oriented basins. The AFT ages range between 215 ± 15 and 80 ± 6 Ma and MTLs are of 9.67–13.13 μm in size from NW Mozambique, with standard deviations of 1.20–2.89 μm. Thermal history modelling indicates long-term cooling of most samples from the latest onset of cooling for samples with standard deviations ca. <2 μm, while older and more complex thermal histories are provided by those with higher standard deviations. Three main exhumation phases are recognized at 300–280 Ma, 200–180 Ma and 100 Ma. The interpreted erosion amounts to about 1.5–3.0 km thick overburden and was triggered by magmatic and tectonic events from pre-, syn- and post-Gondwana break-up. The older cooling event (0.37–0.65 °C/Ma) registered in the northern area includes the period of Karoo type rift basin formation. During this phase between 0.5 and 1.5 km of continental crust was eroded from NW Mozambique and deposited in the Karoo basins. Enhanced erosion at this time was related to the end of Carboniferous-Permian glaciation of Gondwana. The second phase of cooling (0.20–0.50 °C/Ma) marks the onset of Gondwana break-up (ca. 180–190 Ma). At this phase of cooling the currently exposed surface of north Mozambique cooled below 110 ± 10 °C. High sedimentation rates are recorded for the early stages of development of offshore Mozambique basin (ca. 150–180 Ma). The Karoo Supergroup sequences were also sources of sedimentation offshore due to uplift of basin basement. The latter exhumation phase was triggered by epeirogenic uplift from tectonic activity, magmatism and kimberlite intrusion (ca.160–100 Ma). During this event, about 1.0–1.5 km were eroded and deposited over the north of the Mozambique Basin and constrained from increasing sediment supply. [ABSTRACT FROM AUTHOR]