Apatite fission-track analysis was applied to Triassic and Cretaceous sediments from the South-Iberian Continental Margin to unravel its thermal history. Apatite fission-track age populations from Triassic samples indicate partial annealing and point to a maximum temperature of around 100-110°C during their post-depositional evolution. In certain apatites from Cretaceous samples, two different fission-track age populations of 93-99 and around 180 Ma can be distinguished. Track lengths associated with these two populations enabled thermal modelling based on experimental annealing and mathematical algorithms. These thermal models indicate that the post-depositional thermal evolution attained temperatures ≤ 70°C, which is consistent with available vitrinitereflectance data. Thermal modelling for the Cretaceous samples makes it possible to decipher a succession of cooling and heating periods, consisting of (a) a late Carboniferous-Permian cooling followed by (b) a progressive heating episode that ended approximately 120 Ma at a maximum T of around 110°C. The first cooling episode resulted from a combination of factors such as: the relaxation of the thermal anomaly related to the termination of the Hercynian cycle; the progressive exhumation of the Hercynian basement and the thermal subsidence related to the rifting of the Bay of Biscay, reactivated during the Late Permian. Jurassic thermal evolution deduced from the inherited thermal signal in the Cretaceous sediments is characterized by progressive heating that ended around 120 Ma. This heating episode is related to thermal subsidence during Jurassic rifting, in agreement with the presence of abundant mantle-derived tholeiitic magmas interbedded in the Jurassic rocks. The end of the Jurassic rifting is well marked by a cooling episode apparently starting during Neocomiam times and ending at surface conditions by Albian times.