 In July 1861, after Tennessee had seceded, Haynes wrote to Confederate Secretary of War LeRoy P. Walker, warning him that East Tennessee was a hotbed of pro-Union activity, and expressing concerns that Unionists might attack bridges along the critical East Tennessee and Virginia Railroad (the latter of which was realized in November when Union guerrillas destroyed five railroad bridges in the region).He asked that Confederate troops be sent to occupy parts of East Tennessee to discourage Unionists, which Walker granted.On October 24, 1861, the Tennessee General Assembly elected Haynes to one of the state's two seats in the Confederate Senate (the other went to Gustavus A. Henry).