Sedimentary rocks in the Borrego Badlands, Southern California, contain a record of Pleistocene crustal deformation during initiation and evolution of the San Jacinto fault zone. We used detailed geologic, stratigraphic, and paleomagnetic analysis to determine the age and geometry of the deposits and reconstruct the history of fault-controlled sedimentation in this area. The base of the ∼300 to 500 m thick Ocotillo Formation is a paraconformity to abrupt conformable contact that records a brief hiatus followed by rapid progradation of coarse alluvial sediment over lacustrine facies of the Borrego Formation at 1.05 ± 0.03 Ma. This coincides with regional-scale progradation of Ocotillo Formation sand and gravel, and appears to record initiation of strike-slip faults in the southwestern Salton Trough at ca. 1.1 Ma. Thickness trends, clast compositions, paleo-currents, and distribution of paleosols provide evidence for initiation of the East Coyote Mountain fault at ca. 1.05 Ma, followed by onset of NNE-ward basin tilting obliquely toward the Santa Rosa segment of the Clark fault at ca. 1.0 Ma. Stratigraphic omission of the Ocotillo Formation and progressively older units southwest of the Coyote Creek fault beneath the Fonts Point Sandstone provides evidence that tilting to the north-northeast was related in part to growth of the San Felipe anticline during deposition of the Ocotillo Formation. Map and stratigraphic data suggest that the Coyote Creek fault in the western Borrego Badlands postdates Ocotillo deposition, and thus appears to have propagated southeast into the study area at ca. 0.6 Ma. The Fonts Point Sandstone is a thin, sheet-like alluvial deposit that records the end of deposition and onset of transpressive deformation in the Borrego Badlands. The base of the Fonts Point Sandstone changes from a conformable contact in a narrow belt southeast of the Inspiration Point fault, where it is dated at 0.6 ± 0.02 Ma, to an angular unconformity on the folded Ocotillo Formation northwest of the fault. The pattern of stratal truncation records initiation of the Inspiration Point fault at ca. 0.6 Ma. This coincides with a major structural reorganization in the San Jacinto fault zone that initiated the modern phase of north-south shortening and erosion in the southwestern Salton Trough.