Although Jose Rodríguez Cabrillo discovered the area in 1542 and named it San Miguel, the name did not stick. In November of 1602, Sebastian Vizcaíno was mapping the Pacific coast for Spain, and he named the area for the Spanish Catholic saint San Diego de Alcalá. It was not until 1769 that Mission San Diego de Alcala was built in San Diego, in an effort to establish possession of California to prevent Russian settlers from entering the area. The Mission was the first of 21 Missions established throughout California by the Spanish. In 1821, Mexico won its independence from Spain, and California became a territory of Mexico.

Twenty-five years later, during the Mexican-American War, the city of San Diego is captured by a contingent of marines from the U.S.S. Cyane. The rest of California was taken shortly thereafter, and the State became a U.S. possession following the war, along with Arizona, New Mexico, and Texas. Shortly following the discovery of gold outside of San Francisco in 1848, California became the 31st state in the Union.

Following the beginning of the 20th century, the U.S. Navy began to take an interest in San Diego, starting with a Coaling Station. Since then, a total of 19 military bases have been established around San Diego, including the 3rd Fleet Headquarters. Along with the military presence has come a large number of Defence Department related industries. Along with tourism, these two industries have come to dominate the San Diego economy.