For our understanding of the timing and geometry of the initial Gondwana break-up, still a consistent image of the crustal composition of the conjugated margins of central Mozambique and Antarctica and the location of their continent-ocean boundaries is missing. In this regard, a main objective is the explanation for the source of the different magnetic signature of the conjugate margins. Based on a revised investigation of wide-angle seismic data along two profiles across the Mozambican margin by means of an amplitude modelling, this study presents the crustal composition across and along the continental margin of central Mozambique. Supported by 2D magnetic modelling, the results are compared to the conjugate margin in Antarctica and allow new conclusions about their joined tectonic evolution. An observed crustal diversity between the north-eastern and south-western parts of the central Mozambican margin, testifies to the complex break-up history of this area. Conspicuous is the equal spatial extent of the HVLCB along the margin of 190–215 km. The onset of oceanic crust at the central Mozambican margin is refined to chron M38n.2n (164.1 Ma). Magnetic modelling supports the presence of reversed polarized SDRs in the continent-ocean transition that were mainly emplaced between 168.5 and 166.8 Ma (M42–M40). Inferred SDRs in the Riiser-Larsen Sea might be emplaced sometime between 166.8 and 164.1Ma (M39–M38), but got overprinted by normal polarized intrusions of a late stage of rift volcanism, causing the opposite magnetic signature of the conjugate margins. The distribution of the magmatic material along the central coast ofMozambique clearly indicates the eastern extension of the north-eastern branch of the Karoo triple rift along the entire margin. The main magmatic phase affecting this area lasted for at least 12 Myr between 169 and 157Ma, followed by the cease of the magmatism, perhaps due to the relative southwards motion of the magmatic centre.