Basement rocks on the margins of the late Oligocene-Miocene Gulf of Suez-Red Sea rift system contain penetrative west-northwest, northwest, and north-south Precambrian structures, including foliations, fractures, faults, and regional sinistral shear zones. These have been reactivated during the Cenozoic rifting and have exerted fundamental controls on both rift-border fault geometries and the location of accommodation zones within the rift system. Two accommodation zones, the Zaafarana accommodation zone in the northern Gulf of Suez and the Duwi accommodation zone in the northwestern Red Sea rift margin, have been analyzed in detail. In both accommodation zones, the southwest-dipping, eastern rift-border faults (EBFs) consist of reactivated, Precambrian north-south and northwest foliations and fractures, which link together forming a rhomboidal zigzag fault pattern. Each EBF intersects a Precambrian shear zone then splays and loses displacement. In contrast, both of the northeast-dipping, western border faults (WBFs) consist of a reactivated fault segment colinear with a Precambrian shear zone, and this is hard-linked to a north-south-north-northeast-oriented, less well developed fault system via a discrete transfer fault. The change in dip direction of the half grabens is related to initial reactivation of preexisting regional, intersecting north-south and west-northwest Precambrian shear zones by late Oligocene-early Miocene N60 degreesE extension. This configuration allows initial left-lateral and right-lateral oblique-slip on the north-south and west-northwest zones, respectively. We present new models for the localization of the accommodation zones and for the development of the rift half-graben architectures.