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There is physical evidence and written accounts of California Indians over a hundred years before the Spanish arrived. Evidence of tools has been found in various parts of California which have been dated back centuries before European contact.

There are also accounts by European explorers and pirates like Sir Francis Drake, who made contact with Indians before the first mission was established. California Indian oral history dates back much further than European contact.

We do not have any census data that indicates an exact number of Indians living in California.

Missionaries only documents how many Indians were in the missions and speculated about how many Indians lived in the villages surrounding the missions. Many tribes in the north of interior regions of California were untouched by the missions, so the missionaries did not factor in these populations into their calculations. The people who settled in those regions during the gold rush did not keep accurate records of the native populations that they decimated in search of gold.

As a result of these two occupations, native populations were weakened, but neither the Spanish, nor the countless gold miners, kept track of how many Indians lived in California at any one time. Some scientists estimate that there were over 300,000 Indians living in California before the missions were established. Other scientists argue that the 300,000 figure is low and it was more likely to 1,000,000.

Some accounts by Spanish missionaries suggest that Indians were welcoming and willingly entered the missions; however these accounts were highly biased and are most likely false.

In letters to their superiors or to each other, missionaries would have been inclined to make each other believe that Indians had willingly come to the missions in order to make their missions appear to be running smoothly. Missionaries may have also tried to cover up the atrocities that often occurred in the missions. By contrast to their letters, the personal diaries and private accounts of the missionaries suggest that Indians were resistant to mission authorities. Missionaries forbade California Indians from practicing their religion, speaking in their traditional language, and eating their traditional foods. Many Indians who were forced into the missions did attempt to keep their culture alive and were punished cruelly for it. The accounts of Indians being punished by the missionaries suggest that Indians resisted Spanish rule, rather than welcoming it.

Spanish and others had been coming and going in California for over a 150 years. From accounts of some European explorers, we know that Indians traded with Europeans, but we do not know much communication occurred and whether Indians were informed of European intentions. When the Spanish established the first mission in San Diego, the surrounding tribal villages organized a defense strategy on the Spanish camp within one month of their arrival, in an attempt to drive them out of their territory.

Most accounts of Indians life in the missions suggest that Indians were unhappy in the missions because there were mistreated by the priests, restricted from practicing their religions ceremonies and separated from their families. After the first mission that was established in San Diego and the Kumeyaay attempted to defend their within a month of the Spanish encampment.

The padres did not record a baptism for two years. This suggests that the Spanish faced challenges in getting natives to adopt mission life.

Since many Indians resisted life in the missions, there is no evidence that Indians even liked living in the missions, let alone defended them. Some questions come to the surface when asking this questions that reveal the inconsistencies with the claim: Who were they defending the mission from, and why were they loyal to the Spanish? To answer the first question, the Kumeyaay would have been unlikely to defend the mission, since the record reflects resistance. No other European colonies were in the nearby area to attack the mission either.

Without the need for defense, there is little evidence to support this claim. If someone were to attack the mission because they were not treated well. There is evidence to suggest that the Kumeyaay had been involved in several rebellions against the missions indicating that they were more likely to attack the mission than defend it.

Records reflect very few baptisms during the first years of the mission. The low amount of baptisms during the first few years of many missions can be understood as defiance from the tribes around the missions. Many tribes refused to join the mission or resisted the Spanish when they attempted to force tribes to join the missions. The small number of baptisms performed during this time may have sparked an increased effort by the soldiers who came with the missionaries to round up Indians and force them into the missions. Without these numbers, the missions would not have been able to function. These beginning periods serve to debunk the idea that Indians willingly joined the missions or were curious about them. If the tribes did not come to the missions after three years, then they were most likely resisting the padres and soldiers.

In the eyes of the padres, California Indians were considered uncivilized because they looked different, had different religious beliefs and languages, and did not build structures, governing authorities and agriculture or farming practices that were familiar to Europeans; this does not mean that they were civilized. Europeans failed to recognize or acknowledge many of these existing practices. California Indians did make permanent dwelling, practiced (and continue to practice) their own unique religions, use their own languages, cultivated and harvest foods and medicines from their environments, and had governance and political organizations. California Indians were far from uncivilized.

Unfortunately the two words most commonly used to describe Indian contact with the missions are misleading. The term "wander" implies that the Indians casually arrived at the mission without a purpose. Also Implying that they had no purpose before coming to the mission. This was not the case. Indians lived in a subsistence culture, everyday had purpose in providing for their families and community members. They knew the intricate natures of their homelands and did not get lost or wander around. The second term "joined" implied that Indians became members of or enlisted in the mission system, suggesting that it was a voluntary process.

The mission was created under a “feudal manorial labor system” Indians were intended to be “absorbed into Spanish colonial society at the lowest level.” They were forced to labor for Spain for the “good of the Spanish crown it’s citizens.”

Based on the low number of baptisms during the first few years in some missions, Indians may have resisted the missions and the padres, rather than "wandering" over. This idea is often used in romanticized accounts of missions life or the mission system to avoid talking about kidnapping and forced labor, which were tactics used by the padres to bring Indians into the missions as laborers. Missionaries banned Indians from using their traditional languages, practicing religions ceremonies, and eating traditional foods in the missions, which are a few reasons why Indians did not want to join the missions. Although there is no written evidence, California Indians often traded with one another and passed on stories about the poor treatment of other tribes in the missions, Indians were also beaten for small crimes within the missions, contributing to a culture of unnecessary punishment and brutal treatment of Indians by the padres. Even if Indians had "wandered" into the missions, they most likely would not have stayed, or not wanted to stay, because of the harsh treatment that they received.