Natural hydrogen has generated great interest as a potential clean and renewable energy source. To understand the occurrence of natural hydrogen, 103 1-m deep soil gas samples were acquired near the San Andreas Fault at Jasper Ridge and Portola Valley, California, USA. The gas samples were analyzed for hydrogen, helium, carbon dioxide, light hydrocarbons, and fixed gas concentrations. Statistical data analysis was carried out to group samples, reveal their spatial distribution, and understand possible sources of the gases.High concentrations of hydrogen up to 20.3 ppmv and 17.3 ppmv occur in Jasper Ridge and Portola Valley, respectively, ∼30–35 times greater than the atmospheric concentration. Most samples with high hydrogen concentrations fall on or near faults, suggesting an origin by serpentinization or geomechanical activation of catalytic sites in minerals, although a deep-seated primordial origin cannot be excluded. Elevated concentrations of carbon dioxide resulted from aerobic microbial degradation of organic matter and elevated concentrations of light hydrocarbons likely resulted from thermal cracking of organic matter.