The role of lithospheric heterogeneities, presence or absence of melt, local and regional stresses, and gravitational potential energy in strain localization in continental rifts remains debated. We use new seismic and geodetic data to identify the location and orientation of the modern Nubia-Somalia plate boundary in the 300-km-wide zone between the southern Main Ethiopian Rift (MER) and Eastern Rift (ER) across the Mesozoic Anza rift in the Turkana Depression. This region exhibits lithospheric heterogeneity, 45 Ma-Recent magmatism, and more than 1,500 m of base-level elevation change, enabling the assessment of strain localization mechanisms. We relocate 1716 earthquakes using a new 1-D velocity model. Using a new local magnitude scaling with station corrections, we find 1 ≤ ML ≤ 4.5, and a b-value of 1.22 ± 0.06. We present 59 first motion and 3 full moment tensor inversions, and invert for opening directions. We use complementary geodetic displacement vectors and strain rates to describe the geodetic strain field. Our seismic and geodetic strain zones demonstrate that only a small part of the 300 km-wide region is currently active; low elevation and high-elevation regions are active, as are areas with and without Holocene magmatism. Variations in the active plate boundary's location, orientation and strain rate appear to correspond to lithospheric heterogeneities. In the MER-ER linkage zone, a belt of seismically fast mantle lithosphere generally lacking Recent magmatism is coincident with diffuse crustal deformation, whereas seismically slow mantle lithosphere and Recent magmatism are characterized by localized crustal strain; lithospheric heterogeneity drives strain localization.