An aeromagnetic study of the Maiduguri – Dikwa depression in northeastern Nigeria has been carried out to establish its main shallow crustal structural features. The area is intensely fractured with major fractures trending in NE-SW direction. Spectral analysis and 2.0 D modeling of four profiles selected from the residual anomaly map provide depths to basement of 2.82, 3.41, 2.41 and 2.56 km. These depths constrain the magnetic models along the profiles, which indicate that the sedimentary infill is of variable thickness. Thus, we have three sub– basins along the Maiduguri – Dikwa depression: Maiduguri, Mafa-Bama, and Dikwa subbasins. These sub–basins are associated with the extensional tectonics that affected the region from the Benue Trough to the Chad Basin. The Mafa-Bama sub–basin is the deepest one. The sedimentary infill is probably dominated with sandy clayey alluvial deposits, sandstones and shales. Depths to basement were constrained with by spectral analysis results.