The remainder was designated the District of Louisiana and placed under the jurisdiction of Indiana Territory and its governor, William Henry Harrison.

[36] The Confederate government elected two governors, but only had any control in the south of the state, and was forced into exile in Marshall, Texas, after the Battle of Pea Ridge in March 1862.

During the Civil War, after the capture of Jefferson City by the Union, a constitutional convention declared the office then held by Governor Claiborne Fox Jackson to be vacant.

[86] In October, Jackson, Lieutenant Governor Thomas Caute Reynolds, and some members of the General Assembly, organized at Neosho and passed an Ordinance of Secession.

Jackson continued on as governor until his death on December 6, 1862, at which time Reynolds took over, serving until he fled to Mexico in June 1865 after the end of the war.