The 2009 Karonga, Malawi earthquake caused a surface rupture length of 14-18 km along a single W-dipping fault on the hanging wall of the North Basin of the Malawi Rift. This part of the rift is underlain by the NW-trending Precambrian Mughese Shear Zone (MSZ). I used aeromagnetic and electrical resistivity data to elucidate the relationship between surface rupture locations and pre-existing structures. Although several magnetic lineaments are visible in the basement, mapped surface ruptures align with a single 37 km-long, 148°-162° - striking magnetic lineament dipping 40°SW, and is characterized by a zone of electrical disturbance associated with near-surface soil liquefaction features. Fault geometries, regional kinematics and spatial distribution of seismicity suggest that seismogenic faults reactivated the basement fabric found along the half-graben hinge zone. I 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.