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San Clemente Basin is part of the California Continental Borderland. Low temperature hydrothermal alteration is suggested for some minerals. Fe-Mn crusts are hydrogenetic (Fe/Mn = 0.83-1.14), with positive Ce anomaly, but no positive Eu anomaly that would suggest hydrothermal influence. Co is depleted (Co = 0.16-0.23%), probably due to dilution by a terrigenous component. The phosphorite is of high grade (P2O5 = 29%), with high Fe and Ca concentrations compared with other phosphorites from the Baja California Peninsula. It has a typical seawater-type REE pattern, and a significant negative Ce anomaly, which is indicative of outer shelf conditions for the San Clemente Basin during the Miocene. No lithologic evidence is found to suggest ophiolite-type rocks, as occurs in the nearby Santa Cruz and San Nicolás Basins. [ABSTRACT FROM AUTHOR]