He served as the Confederacy's territorial governor for Arizona Territory - a region encompassing the southern half of the modern states of New Mexico and Arizona . At one point his frustration with attacks from Apache tribes grew so great that he ordered their extermination:
There is no indication that his officers followed this order. When news of the order reached Confederate President Jefferson Davis he immediately relieved Baylor of his post of governor. Baylor later enlisted as a private and was elected to the Confederate Congress. He gained a commission of Colonel just before the surrender of CSA forces. After the war he ranched in Texas and participated in more than one deadly fight.