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John Wilson Shaffer (July 5, 1827 – October 31, 1870) was an American politician and businessman.
Born in Lewisburg, Pennsylvania, Shaffer was active in Republican politics in Illinois. In 1849, Shaffer settled in Freeport, Illinois and was involved in the mercantile business. Then, in 1856, he was elected sheriff of Stephenson County, Illinois. He was elected clerk and recorder for the Illinois Circuit Court for Stephenson County. Shaffer served in the 15th Illinois Volunteer Infantry Regiment during the American Civil War and was the quartermaster. He was appointed governor of the territory of Utah by President Ulysses S. Grant. He was known for his strict opposition of any hint of rebellion against the federal government, which led to concerns with the Mormon population. He died suddenly during his first year as governor.