The first European to explore the future Ensenada, was Juan Rodriguez Cabrillo of Portugal, who originally named the area, "San Mateo" (St. Matthew) in 1542. Not to be outdone, Spanish explorer Sebastian Vizcaino "rediscovered" the area 60 years later in 1602, and gave it the name, "Ensenada de Todos Los Santos," which, thankfully,  was shortened to its present moniker. Interestingly, neither of these explorers reported any signs of habitation at these times. A priest, however, traveling to San Diego in 1769, noted the presence of people.

For many years, the area was generally avoided as a place of habitation and consisted mostly of adobe missions.

In 1821, Mexico gained its independence from Spain and California. In 1848, California was divided when the U.S. government paid Mexico $15 million dollars for what became known as Alta California. Baja California remained in Mexican hands and is the northernmost frontier of the Mexican Republic.

In 1854, rich man, William Walker and his hires soldiers arrogantly invaded the territory, but was soundly overcome under the Mexican leadership of Mexican, Antonio Melendres. By the end of American Civil War, in 1865, Baja had begun to attract gold-seekers after the discovery of the metal in San Rafael.

1887 saw the beginnings of Ensenada, by then with an estimated population of between 300 and 440. Another gold rush in 1889 brought more people, but the economy soon bottomed out again. However, mining has remained an industry of the area.

Today, industry, fishing, and tourism encapsulates Ensenada's importance. Its population of over 250,000 swells during the height of tourist seaon.