The Cenozoic East African Rift System (EARS) is an exceptional example of active continental extension, providing opportunities for furthering our understanding of hydrocarbon plays within rifts. It is divided into structurally distinct western and eastern branches. The western branch comprises deep rift basins separated by transfer zones, commonly localised onto pre-existing structures, offering good regional scale hydrocarbon traps. At a basin-scale, local discrete inherited structures might also play an important role on fault localisation and hydrocarbon distribution. Here, we consider the evolution of the Central basin of the Malawi Rift, in particular the influence of pre-existing structural fabrics.Integrating basin-scale multichannel 2D, and high resolution seismic datasets we constrain the border, Mlowe-Nkhata, fault system (MNF) to the west of the basin and smaller Mbamba fault (MF) to the east and document their evolution. Intra basin structures define a series of horsts, which initiated as convergent transfers, along the basin axis. The horsts are offset along a NE-SW striking transfer fault parallel to and along strike of the onshore Karoo 2 (Permo-Triassic) Ruhuhu graben. Discrete pre-existing structures probably determined its location and, oriented obliquely to the extension orientation it accommodated predominantly strike-slip deformation, with more slowly accrued dip-slip.To the north of this transfer fault, the overall basin architecture is asymmetric, thickening to the west throughout; while to the south, an initially symmetric graben architecture became increasingly asymmetric in sediment distribution as strain localised onto the western MNF. The presence of the axial horst increasingly focussed sediment supply to the west. As the transfer fault increased its displacement, so this axial supply was interrupted, effectively starving the south-east while ponding sediments between the western horst margin and the transfer fault. This asymmetric bathymetry and partitioned sedimentation continues to the present-day, overprinting the early basin symmetry and configuration. Sediments deposited earlier become increasingly dissected and fault juxtapositions changed at a small (10-100 m) scale. The observed influence of basin-scale transfer faults on sediment dispersal and fault compartmentalisation due to pre-existing structures oblique to the extension orientation is relevant to analogous exploration settings.