Before the arrival of the first European settlers, the San Benito County area was inhabited by the Mutsun sub-group of the Ohlone Native Americans. In 1772 Father Juan Crespí conducted a brief expedition into the area and named a small river which he found in honor of San Benito de Nursia (Saint Benedict), the patron saint of monasticism. The county was later named after the San Benito Valley, the valley surrounding this river. Thus it was from the Spanish version of the saint’s name that the county eventually took its name.

In 1797 Spanish missionaries founded the first European settlement in the county as the San Juan Bautista mission. In 1848 the United States government gained control over what would soon become the state of California, which included the area now known as San Benito county. The town of New Idria was the next town to develop in the area and was founded ca. 1857. New Idria was centered around the New Idria Mercury Mine. When the mine played out fairly recently in 1972, New Idria was abandoned, and the town is now one of California’s many ghost-towns.

The town of Hollister was founded on November 19, 1868, by William Welles Hollister on the grounds of the former Mexican land-grant Rancho San Justo. In 1874 the California legislature formed San Benito County from a section of Monterey County while naming Hollister as the new county seat. Sections of Merced and Fresno Counties were also later reassigned to San Benito County in 1887 as a result of the growth of the New Idria community. Other towns in the county which were founded early in the county’s history include Tres Pinos and Paicines.