 In January 1861, following Abraham Lincoln's victory, Haynes joined a growing chorus of Tennesseans who called for the state to align itself with the burgeoning Confederate States of America.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.