The most commonly accepted model of migration to the New World is that people from Asia crossed the Bering land bridge to the Americas some 16,500 years ago. The remains of Arlington Springs Man on Santa Rosa Island are among the traces of a very early habitation, dated to the Wisconsin glaciation (the most recent ice age) about 13,000 years ago.

Prior to European contact, some 30 tribes or culture groups lived in what is now California, gathered into perhaps six different language family groups. These groups included the early-arriving Hokan family (winding up in the mountainous far north and the Colorado River basin in the south) and the later-arriving Uto-Aztecan of the desert southeast. The California region contained the highest Native American population density north of what is now Mexico. Because of the temperate climate and easy access to food sources, approximately one-third of all Native Americans in the United States were living in the area of California.

Early Native Californians were hunter-gatherers, with seed collection becoming widespread around 9,000 BCE. Due to the local abundance of food, tribes never developed agriculture or tilled the soil. Two early southern California cultural traditions include the La Jolla complex and the Pauma Complex, both dating from c. 6050–1000 BCE. From 3000 to 2000 BCE, regional diversity developed, with the peoples making fine-tuned adaptations to local environments. Traits recognizable to historic tribes were developed by approximately 500 BCE.

The indigenous people practiced various forms of sophisticated forest gardening in the forests, grasslands, mixed woodlands, and wetlands to ensure availability of food and medicine plants. They controlled fire on a regional scale to create a low-intensity fire ecology; this prevented larger, catastrophic fires and sustained a low-density "wild" agriculture in loose rotation. By burning underbrush and grass, the natives revitalized patches of land and provided fresh shoots to attract food animals. A form of fire-stick farming was used to clear areas of old growth to encourage new in a repeated cycle; a permaculture.