This work presents an experimental and theoretical identification of defects and morphologies of a high-angle near-90° tilt Si boundary created by direct wafer bonding. Two samples with different twist misorientations, between the layer and the (0 0 1) substrate, were studied using conventional transmission electron microscopy (TEM) and geometric phase analysis of high-resolution TEM images. The O-lattice theory was used for atom reconstruction of the interface along the direction. It is demonstrated that to preserve covalent bonding across the interface, it should consist of facets intersected by maximum of six planes with three 90° Shockley dislocations per facet. It is shown that a particular atom reconstruction is needed at transition points from one facet to another. The presence or absence of deviation from exact 90° tilt of the layer with respect to the substrate is shown to be related directly to the undulations of the interface. It is demonstrated that the latter has an influence on the Burgers vector of the dislocations adjusting in-plane twist misorientation. A general model for cubic face-centered materials for an arbitrary 〈1 1 0〉sub,lay tilt interface is proposed, which predicts the net Burgers vector and the spacing between dislocations necessary to realize transition from the lattice of the substrate (layer) to the layer (substrate).