The Hayward and Calaveras Faults, two strike-slip faults of the San Andreas System located in the East San Francisco Bay Area, are commonly considered independent structures for seismic hazard assessment. We use Interferometric Synthetic Aperture RADAR to show that surface creep on the Hayward Fault continues 15 km farther south than previously known, revealing new potential for rupture and damage south of Fremont. The extended trace of the Hayward Fault, also illuminated by shallow repeating micro-earthquakes, documents a surface connection with the Calaveras Fault. At depths greater than 3–5 km, repeating micro-earthquakes located 10 km north of the surface connection highlight the 3-D wedge geometry of the junction. Our new model of the Hayward and Calaveras Faults argues that they should be treated as a single system with potential for earthquake ruptures generating events with magnitudes greater than 7, posing a higher seismic hazard to the East San Francisco Bay Area than previously considered.