The geological structures buried in the Mexicali Valley need to be better constrained. The Calipatria Fault is an essential key as it could represent an old strand of the San Andreas Fault system. Previous and two new seismic profiles in the Mexicali Valley and Altar Desert have been processed and interpreted. Chaotic and Low Amplitude Seismic Anomalies (CLASA) observed in the seismic profiles have revealed the Calipatria Deformation Zone, showing a high correlation with gravity maxima. This correlation could extend to the Salton Sea, resulting in an ancient plate boundary connected to the Southern San Andreas Fault. We propose that this deformation zone is a transtension region due to the change from an orthogonal rifting to an oblique rifting similar to the observations on analog models based on the northern Gulf of California. This change in the rifting style produced narrow basins that facilitated continental breakup observed on magnetic anomalies and deep wells penetrating igneous rocks.