In 1860 Wharton served as a Breckinridge presidential elector and later represented Brazoria County at the state Secession Convention, voting for secession. In addition to his career in law and politics, Wharton was also a planter of considerable means. The 1860 tax roll for Brazoria County showed that he owned $167,004 of taxable property, including 135 slaves. When the war began Wharton was elected captain of Company B, Eighth Texas Cavalry, better known as Terry's Texas Rangers. He rose to command the regiment after the deaths of Col. Benjamin F. Terry and Lt. Col. Thomas S. Lubbock. Wharton led his troop with distinction at the battle of Shiloh, where he was wounded. His leadership in the course of Gen. Braxton Bragg's 1862 Kentucky invasion earned him a promotion to the rank of brigadier general on November 18, 1862. His actions at the battle of Chickamauga in the fall of 1863 earned him another promotion, to the rank of major general.
In February 1864 the general was transferred to Richard Taylor's Trans-Mississippi Department in Louisiana. Upon his arrival he was assigned to lead the cavalry and took part in the closing scenes of the Red River campaign. On April 6, 1865, while visiting Gen. John B. Magruder's headquarters at the Fannin Hotel in Houston, Wharton was killed by fellow officer George W. Baylor in a personal quarrel that grew out of "an unpleasant misunderstanding over military matters." Even though Wharton was found to have been unarmed, Baylor was acquitted of murder charges in 1868. Wharton was originally buried at Hempstead but was later moved to the State Cemetery in Austin.
30° 15.904, -097° 43.603
Texas State Cemetery