Digital mosaics of swath and conventional bathymetry data reveal large, distinct near-circular crater structures in the Inner Continental Borderland offshore southern California. Two have maximum crater diameters that exceed 30 km and a third has a crater diameter of approximately 12 km. All three features exhibit the morphology of large complex craters (raised outer rim, ring moat and central uplift) yet their exact origin remains a mystery. Preliminary analyses of available seismic, gravity and magnetic data over these structures reveal both similarities and distinct differences in geometry, structure and geophysical signature to known impact sites. All three crater structures, however, occur within the Catalina terrane, a highly extended volcanic and metamorphic province floored by Catalina schist basement. A likely alternative origin may thus involve explosive volcanism, caldera collapse and resurgent magmatism, and/or possibly plutonism and schist remobilization associated with the Catalina terrane. No single model for crater formation, whether impact, caldera or pluton, fully accounts for all of the present observations regarding the morphology, internal structure and known geology of these near-circular features. Timing of crater formation post-dates the initial rifting and rotation of the western Transverse Ranges, and appears to predate major right slip along the San Clemente and San Diego Trough fault systems—or approximately 18 to 16 Ma. Regardless of their origin, these complex craters represent some of the largest structures of their kind in western North America and provide a unique opportunity to better understand the development of unusual crater structures in a submarine environment.