During the American Civil War, he was a senior officer of the Confederate States Army who commanded cavalry in the Trans-Mississippi Theater.

[3] U.S. Representative John S. Phelps appointed Marmaduke to the United States Military Academy, from which he graduated in 1857, placing 30th out of 38 students.

[4] Governor Jackson left Jefferson City, Missouri, in June, along with State Guard commander Major-General Sterling Price, to recruit more troops.

Within a short time, Price and Jackson left, leaving Marmaduke in charge of a small force of militia.

Marmaduke's troops were not adequately prepared for combat, but Governor Jackson ordered him to stand against U.S. forces who had entered the state.

U.S. brigadier-general Nathaniel Lyon's 1,700 well-trained and equipped soldiers easily routed Marmaduke's untrained and poorly armed force at the Battle of Boonville on June 17, 1861.

The skirmish was mockingly dubbed "the Boonville Races" by Unionists because Marmaduke's forces broke and ran after 20 minutes of battle.

In September 1863, he accused his immediate superior officer, Brigadier-General Lucius M. Walker, of cowardice in action for not being present with his men on the battlefield.

While commanding a mixed force of Confederate troops, including Native-American soldiers of the 1st, and 2nd Choctaw Regiments, he defeated a U.S. foraging detachment at the Battle of Poison Spring, Arkansas, on April 18, 1864.

[7] His younger brother, Henry Hungerford Marmaduke, who was in the Confederate States Navy, was captured and imprisoned on Johnson's Island.

[9] Marmaduke decided to enter politics but lost the 1880 Democratic nomination for governor to the former U.S. general Thomas Theodore Crittenden, who had strong support and financial backing from the railroads.

Marmaduke conducted a campaign that highlighted his Confederate service, emphasized abuses of Missourians by U.S. soldiers during the Civil War, celebrated the activities of pro-Confederate "partisan guerrillas" such as William Clarke Quantrill, and claimed that the Republican Party in Missouri was a tool of "carpetbaggers" to oppress "native" Missourians.