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The town was originally named Moore's Station after its chief landowner. It was renamed Boone's Station and then Booneville in honor of the American frontiersman, Daniel Boone. The town, consisting at the time of little more than a temporary log courthouse, became the county seat when Owsley County was formed on May 20, 1844. From this, the settlement was also sometimes known as Owsley Court House around this time. It was formally incorporated as a city by the state assembly on March 1, 1847.