We integrated temporal aeromagnetic data and recent earthquake data to address the long‐standing question on the role of preexisting Precambrian structures in modulating strain accommodation and subsequent ruptures leading to seismic events within the East African Rift System. We used aeromagnetic data to elucidate the relationship between the locations of the 2009 Mw 6.0 Karonga, Malawi, earthquake surface ruptures and buried basement faults along the hinge zone of the half‐graben comprising the North Basin of the Malawi Rift. Through the application of derivative filters and depth‐to‐magnetic‐source modeling, we identified and constrained the trend of the Precambrian metamorphic fabrics and correlated them to the three‐dimensional structure of buried basement faults. Our results reveal an unprecedented detail of the basement fabric dominated by high‐frequency WNW to NW trending magnetic lineaments associated with the Precambrian Mughese Shear Zone fabric. The high‐frequency magnetic lineaments are superimposed by lower frequency NNW trending magnetic lineaments associated with possible Cenozoic faults. Surface ruptures associated with the 2009 Mw 6.0 Karonga earthquake swarm aligned with one of the NNW‐trending magnetic lineaments defining a normal fault that is characterized by right‐stepping segments along its northern half and coalesced segments on its southern half. Fault geometries, regional kinematics, and spatial distribution of seismicity suggest that seismogenic faults reactivated the basement fabric found along the half‐graben hinge zone. We suggest that focusing of strain accommodation and seismicity along the half‐graben hinge zone is facilitated and modulated by the presence of the basement fabric.

We used detailed analysis of Shuttle Radar Topography Mission-digital elevation model and observations from aeromagnetic data to examine the influence of inherited lithospheric heterogeneity and kinematics in the segmentation of largely amagmatic continental rifts. We focused on the Cenozoic Malawi Rift, which represents the southern extension of the Western Branch of the East African Rift System. This north trending rift traverses Precambrian and Paleozoic-Mesozoic structures of different orientations. We found that the rift can be hierarchically divided into first-order and second-order segments. In the first-order segmentation, we divided the rift into Northern, Central, and Southern sections. In its Northern Section, the rift follows Paleoproterozoic and Neoproterozoic terrains with structural grain that favored the localization of extension within well-developed border faults. The Central Section occurs within Mesoproterozoic-Neoproterozoic terrain with regional structures oblique to the rift extent. We propose that the lack of inherited lithospheric heterogeneity favoring extension localization resulted in the development of the rift in this section as a shallow graben with undeveloped border faults. In the Southern Section, Mesoproterozoic-Neoproterozoic rocks were reactivated and developed the border faults. In the second-order segmentation, only observed in the Northern Section, we divided the section into five segments that approximate four half-grabens/ asymmetrical grabens with alternating polarities. The change of polarity coincides with flip-over full-grabens occurring within overlap zones associated with~150 km long alternating border faults segments. The inherited lithospheric heterogeneity played the major role in facilitating the segmentation of the Malawi Rift during its opening resulting from extension. Key Points:• Segmentation of the Malawi Rift is studied using SRTM DEM and magnetic data • The rift is hierarchically divided into first-order and second-order segments • Lithospheric heterogeneity controls firstand second-order segmentation

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