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Source: California Indian Wars

The California Indian Wars were a series of wars, battles, and massacres between the United States Army (or often the California State Militia, especially during the early 1850s), and the Indigenous peoples of California. The wars lasted from 1850, immediately after Alta California, acquired during the Mexican–American War, became the state of California, to 1880 when the last minor military operation on the Colorado River ended the Calloway Affair of 1880.
Following the acquisition of the Mexican Cession in the Treaty of Guadalupe Hidalgo that ended the Mexican–American War, the small Federal garrison west of the Rocky Mountains was spread out over that vast territory. Shortly afterward, the economic effects of the California Gold Rush encouraged desertions that further weakened the garrisons within the territory of California. Following statehood, the California State Militia engaged in most of the early conflicts with the Indians within its boundaries before the American Civil War. The state sought compensation from the United States federal government for the cost of the operations and for the "depredations" of the Indians, claims that would not be settled for decades. Often, a number of miners or other settlers, who were impatient at the bureaucratic delay or political opposition involved with organizing militia companies, organized themselves to violently engage local Indian tribes, at times murdering several of its members, indiscriminately.
Later during the American Civil War, California and Oregon State Volunteers replaced Federal troops west of the Rocky Mountains and engaged in many conflicts with the Indians in that region including in California, Nevada and Utah, New Mexico and Arizona Territories. Within California they fought in the ongoing 1858-1864 Bald Hills War and in the 1862-1863 Owens Valley Indian War. Minor skirmishes occurred between local militias or volunteers and the Yahi, Yana and Paiute in northeastern California into the 1870s. Following the Civil War, most hostilities in California were over except for a few minor skirmishes in the Owens Valley and in the Mojave Desert against the Timbisha and Chemehuevi. Federal troops replaced the volunteers between late 1865 and early 1866 and again engaged in military actions in the remote regions of the Mojave Desert, Owens Valley and the northeast of the state against the Snakes and later the Modoc in the next two decades.