In November 1847, Charbonneau accepted an appointment from Colonel John D. Stevenson as alcalde (mayor) at Mission San Luis Rey de Francia. This position made him the only civilian authority, a combined sheriff, lawyer and magistrate, in a post-war region covering about 225 square miles (580 km2). From 1834–50, the lands were owned by rancheros through legally questionable land-grants.
The rancheros hired local American Indians, mainly Luiseño, to do agricultural work. Many functioned in virtual servitude, and some rancheros paid them only with liquor. Trying to correct abuses and also facilitate post-war control, in November 1847, Colonel Richard Barnes Mason, the territorial governor, ordered Charbonneau to force the sale of a large ranch owned by the powerful Jose Antonio Pico, whose family was politically connected. His brother Pio Pico had been the last governor of California under Mexico. On January 1, 1848, Mason banned the sale of liquor to Indians. Such ordinances attacked the foundation of ranchero power and ability to do business. Eventually the changes led to United States civilian control of California. Although Charbonneau was assisted by Captain J. D. Hunter as he negotiated with Pico, he saw that local resistance would make enforcing Mason's orders difficult. Charbonneau resigned his post in August 1848, and was soon followed by Hunter. California statehood on September 9, 1850, ended the post-war difficulties.
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