Gihon bm.  Thompson was a lieutenant-colonel in the Missouri state militia at the outbreak of the Civil War. On July 25, 1861, he was appointed brigadier-general of the 1st Division, Missouri State Guard. He commanded the First Military District of Missouri, which covered the swampy southeastern quarter of the state from St. Louis to the Mississippi River. Thompson's battalion soon became known as the "Swamp Rats" for their exploits. He gained renown as the "Swamp Fox of the Confederacy." Although Thompson frequently petitioned for the Confederate rank of brigadier-general it was never granted. His brigadier rank came from his Missouri State Guard service.[4]When Union Major-General John C. Fremont issued an emancipation proclamation purporting to free the slaves in Missouri, Thompson declared a counter-proclamation and his force of 3,000 soldiers began raiding Union positions near the border in October. On October 15, 1861, Thompson led a cavalry attack on the Iron Mountain Railroad bridge over the Big River near Blackwell in Jefferson County. After successfully burning the bridge, Thompson retreated to join his infantry in Fredericktown. Soon afterwards, he was defeated at the Battle of Fredericktown and withdrew, leaving southeastern Missouri in Union control.After briefly commanding rams in the Confederate riverine fleet in 1862, Thompson was reassigned to the Trans-Mississippi region. There, he engaged in a number of battles before returning to Arkansas in 1863 to accompany Gen. John S. Marmaduke on his raid into Missouri. Thompson was captured in August in Arkansas, and spent time in St. Louis' Gratiot Military Prison, as well as at the Fort Delaware and Johnson's Island prisoner-of-war camps ("Poor old Jeff, how my heart went out to him; he a prisoner and his devoted wife in a madhouse", Major Lamar Fontaine wrote later).[5]Thompson as a POW c. 1864Eventually, he was exchanged in 1864 for a Union general. Later that year, Thompson participated in Major-General Sterling Price's Missouri expedition, taking command of "Jo" Shelby's famed "Iron Brigade" when Shelby became division commander. He served competently in this role.In March 1865, Thompson was appointed commander of the Northern Sub-District of Arkansas. He agreed to surrender his command at Chalk Bluff, Arkansas on May 11, 1865.[6][7]