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At the time of European encounter, Clarke County was the traditional home of the Choctaw and the Creek people. They traded with the French, who had settlements in Mobile and New Orleans. They also were reached by some English and Scots traders from the British colonies along the Atlantic Coast. After the Louisiana Purchase, they started to establish relations with the United States.
In 1805, by the Treaty of Mount Dexter, the Choctaw conveyed large amounts of land in what is now southeastern Mississippi and southwestern Alabama, including much of the western portion of Clarke County, to the United States for settlement by European Americans.
Clarke County was established on December 10, 1812, by the Mississippi Territory. The county had numerous forts, built by settlers for protection during the Creek War (1813–1814). Some of these forts included: Fort Carney, Fort Easley, Fort Glass, Fort Landrum, Fort Madison, and Fort Sinquefield. The first county seat was Clarkesville, founded in 1820. The seat was moved to Macon, later renamed Grove Hill, in 1831. During the American Civil War, the county was notable for its salt production. The county is named for Georgia Gov. John Clarke.
In 1883, the U.S. Supreme Court upheld the conviction of Tony Pace and Mary Cox for interracial dating, in Pace v. Alabama. That precedent was subsequently overturned. In 1892, Clarke County was the scene of a violent confrontation around economic divides that later became known as the Mitcham War.
Following the national repeal of prohibition in 1933, Clarke County voted to become a dry county in 1937, when wet-dry counties were established in Alabama.
In the first decade of the 21st century, the county's largest communities voted to legalize alcohol sales: Jackson on May 10, 2005; Thomasville on August 14, 2007; and Grove Hill on November 3, 2009.