The San Diego trough fault zone (SDTFZ) is part of a 90‐km‐wide zone of faults within the inner California Borderland that accommodates motion between the Pacific and North American plates. Along with most faults offshore southern California, the slip rate and paleoseismic history of the SDTFZ are unknown. We present new seismic reflection data that show that the fault zone steps across a 5‐km‐wide stepover to continue for an additional 60 km north of its previously mapped extent. The 1986 Oceanside earthquake swarm is located within the 20‐km‐long restraining stepover. Farther north, at the latitude of Santa Catalina Island, the SDTFZ bends 20° to the west and may be linked via a complex zone of folds with the San Pedro basin fault zone (SPBFZ). In a cooperative program between the U.S. Geological Survey (USGS) and the Monterey Bay Aquarium Research Institute (MBARI), we measure and date the coseismic offset of a submarine channel that intersects the fault zone near the SDTFZ–SPBFZ junction. We estimate a horizontal slip rate of about 1.5±0.3 mm/yr over the past 12,270 yr.