In November 1861 he was elected as a Democrat to the state Senate. Although a Unionist, he resigned from the Senate and on March 20, 1862, enlisted in the Confederate Army. A month later he was elected captain of Company A in Col. George Washington Carter's Twenty-first Texas Cavalry. On August 3, 1863, Branch defeated Peter W. Gray in the race to represent the Third District of Texas in the Second Confederate Congress. In Richmond he served as a member of the Elections, Military Affairs, and Territories and Public Lands committees and was vitally interested in the exportation of cotton through Mexican ports. Although a staunch political ally of President Jefferson Davis, Branch was an uncompromising exponent of states' rights. As such he fought to keep Texas troops in Texas and opposed Confederate interference with the Texas economy. After the war he returned to Texas and was elected to the United States House of Representatives in both the Thirty-ninth and Fortieth congresses but was denied his seat by the Radical Republican majority. He returned to Huntsville and helped to incorporate the Central Transit Company in 1866. Branch practiced law until his death during a yellow fever epidemic, on October 3, 1867. He is buried in Oakwood Cemetery near the grave of Sam Houston.
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