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The original Rowan County courthouse was located along Main Street in Morehead, Kentucky. During the Civil War, it was burned and destroyed by a pro-Confederate guerrilla group. The courthouse was later rebuilt during the Reconstruction era, in its original location. In 1880, however, leading up to the Rowan County War, the courthouse was once again burned during a fight between the county's two opposing factions. As a result of both burnings, all legal records prior to 1880 were lost.

Over the course of the Civil War, the state of Kentucky suffered the loss of numerous state buildings and the destruction of a great deal of historical architecture. One of the most frequent sites targeted during the war were the various county courthouses located throughout Kentucky, as they housed historical records and stood as symbols of authority. Consequently, twenty-two courthouses were burned during the Civil War - nineteen of which were targeted during the last fifteen months of the war alone - at the behest of both Union and Confederate leaders alike. In addition to the leaders of these two opposing forces, the burning of courthouses was often carried out by pro-Confederate guerrilla groups. One such group was based in Morehead, Kentucky, part of Rowan County, during the Civil War. On March 21, 1864, the guerrilla group carried out the burning of the Rowan County courthouse, based in Morehead, launching flaming torches at the building until it was wholly engulfed in flames. This burning marked the easternmost attack on an institution in the state of Kentucky during the war. 

After the end of the Civil War, during the era of Reconstruction, Kentucky worked to rebuild what had been destroyed by the acts of violence carried out during the war. Subsequently, the courthouse was rebuilt, with construction completed on the new building in 1866. The courthouse stood in place of the previous building in Morehead for nearly fourteen years until the events leading up to the Rowan County War. The Rowan County War was fought after an intense and contested run for county sheriff between two warring factions, with the city of Morehead acting as the epicenter of the war. This lead to a three-year period of lawlessness within the county. With its centrality to the events of the small-scale war, Morehead was the Rowan County city most afflicted by the acts of violence carried out during the fighting. The county courthouse, located in Morehead, once again became collateral damage, being burned again in 1880 during a small skirmish between the county's feuding factions. 

After this, the courthouse was relocated to another building until it was eventually rebuilt again in 1899. As a result of each of the two burnings, all of the legal records housed in the courthouse prior to 1880 were destroyed, with no way to recover them. 

Kentucky Courthouse Burnings. Accessed August 06, 2019.

Rowan County Courthouse Burned. Accessed August 06, 2019.