The first people came to the peninsula at least 11,000 years ago. At that time two main native groups are thought to have been present on the peninsula. In the south were the Cochimí. In the north were several groups belonging to the Yuman language family, including the Kiliwa, Paipai, Kumeyaay, Cocopa, and Quechan. These peoples were diverse in their adaptations to the region. The Cochimí of the peninsula's Central Desert were generalized hunter-gatherers who moved frequently; however, the Cochimí on Cedros Island off the west coast had developed a strongly maritime economy. The Kiliwa, Paipai, and Kumeyaay in the better-watered northwest were also hunter-gatherers, but that region supported denser populations and a more sedentary lifestyle. The Cocopa and Quechan of northeastern Baja California practiced agriculture in the floodplain of the lower Colorado River.
Another group of people were the Guachimis, who came from the north and created much of the Sierra de Guadalupe cave paintings. Not much is known about them except that they lived in the area between 100 BC and the coming of the Europeans and created World Heritage rock art.
Europeans reached the present state of Baja California in 1539, when Francisco de Ulloa reconnoitered its east coast on the Gulf of California and explored the peninsula's west coast at least as far north as Cedros Island. Hernando de Alarcón returned to the east coast and ascended the lower Colorado River in 1540, and Juan Rodríguez Cabrillo (or João Rodrigues Cabrilho (in Portuguese)) completed the reconnaissance of the west coast in 1542. Sebastián Vizcaíno again surveyed the west coast in 1602, but outside visitors during the following century were few.
The Jesuits founded a permanent mission colony on the peninsula at Loreto in 1697. During the following decades, they gradually extended their sway throughout the present state of Baja California Sur. In 1751–1753, the Croatian Jesuit mission-explorer Ferdinand Konščak made overland explorations northward into the state of Baja California. Jesuit missions were subsequently established among the Cochimí at Santa Gertrudis (1752), San Borja (1762), and Santa María (1767).
After the expulsion of the Jesuits in 1768, the short-lived Franciscan administration (1768–1773) resulted in one new mission at San Fernando Velicatá. More importantly, the 1769 expedition to settle Alta California under Gaspar de Portolà and Junípero Serra resulted in the first overland exploration of the northwestern portion of the state.
The Dominicans took over management of the Baja California missions from the Franciscans in 1773. They established a chain of new missions among the northern Cochimí and western Yumans, first on the coast and subsequently inland, extending from El Rosario (1774) to Descanso (1817), just south of Tijuana.
19th and 20th centuries
- The colonial governors were:
- 1833: Mexican secularization act of 1833
- 1848: Alta California is annexed by the United States.
- 1853: Soldier of fortune William Walker captures La Paz, declaring himself President of the Republic of Lower California. The Mexican government forces his retreat after several months.
- 1884: Luis Huller and George H. Sisson obtain a concession covering much of the present state, in return for promises to develop the area.
- 1905: The Magonista revolution, an anarchist movement based on the writings of Ricardo Flores Magón and Enrique Flores Magón, begins.
- 1911: Mexicali and Tijuana are captured by the Mexican Liberal Party (Partido Liberal Mexicano, PLM), but soon surrender to Federal forces.
- 1917: On 11 December, "[a] prominent Mexican, close friend of President Carranza" offered to U. S. Senator Henry Ashurst to sell Baja California to the U. S. for "fifty million dollars gold."
- 1930: Baja California is further divided into Northern and Southern territories.
- 1952: The North Territory of Baja California becomes the 29th state of Mexico, Baja California. The southern portion, below 28°N, remains a federally administered territory.
- 1974: The South Territory of Baja California becomes the 31st state, Baja California Sur.
- 1989: Ernesto Ruffo Appel of the PAN becomes the first non-PRI governor of Baja California and the first opposition governor of any state since the Revolution.