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Mission structure
The hierarchy of power in missions was a major cause of culture clash between Franciscan missionaries and Native Americans. Missionaries delineated authority to Native American officials who often held power within their own tribes, but this authority clashed with their own cultural values. While social organization in precontact California is scarcely recorded, but a ruling elite presided over commoners and an underclass, determined by lineage and cultural inheritance. Conversely, mission power structure was determined by elections, eliminating traditional Native American social hierarchy and replacing it with a system heavily monitored and often controlled by Franciscans.

Native American officials were often tasked with keeping the peace between missionaries and Native American inhabitants, leading to increased friction between officials and their unelected counterparts. Regarding the duty of officials, Junípero Serra wrote in a letter to his trusted subordinate Fermín Lasuén: "Ask him to carry out this function so that, without failing in the slightest degree in his duty toward his superior officer, the Indians may not be given a less exalted opinion of the fathers than they have had until now."

The canonization of Junípero Serra continues to spark contemporary debate regarding the treatment of Native Americans at the hands of Franciscan missionaries. In reaction to Pope Francis's announcement that he would canonize Serra in January of 2015 was, a statue of Christ in a cemetery at Mission San Gabriel in Los Angeles was toppled, and a MoveOn petition to "enlighten" the pope regarding “the deception, exploitation, oppression, enslavement, and genocide” of Native Americans received over 10,000 signatures.