This study attempts to delineate subsurface lineaments for the tectonically and volcanically active region of the Ziway-Shala Lakes basin, central Main Ethiopian rift. Most of the previously mapped subsurface structures in the region under consideration focus on delineating crustal structures thicknesses and Moho depths undulations. Moreover, near-surface structures in the same region were mapped using analysis of Digital Elevation Model image data. On the other hand, there are few studies that have targeted in mapping geologic structures lying at intermediate depth levels between the shallower and deeper Earth. The objective of this research is thus to map the subsurface geologic structures/lineaments to an average depth of 3 km (crystalline basement layer depth) from surface using gravity data. These investigation results are validated by Digital Elevation Model extracted lineaments. Filtering techniques including derivative filters, upward-continuation and line module algorithm of PCI Geomatica are used to extract the gravity and topographic lineaments of the region. Orientation analyses of these subsurface and surface lineaments are made using line direction histogram of the QGIS software. Accordingly, the gravity subsurface lineaments mapped in this study are found to be dominantly oriented in the NNW-SSE to NW-SE and E-W direction on average. These results appear to be contrary to the NNE-SSW to NE-SW trending surface geologic structure mapped on the bases of actual field observation carried out by previous researchers and automatically extracted lineaments based on Digital Elevation Models data considered in this research. The subsurface lineaments mapped using gravity data coincide with the orientation of pre-existing subsurface structures crossing the rift orthogonally. These structural lineaments which are considered to be masked in the subsurface coincide with the orientation of the Mesozoic Ogaden rift as compared to the overlying surface structures which appear to coincide with the orientation of the Cenozoic Main Ethiopian rift.