During the American Civil War, Gray was a steadfast supporter of the North and the Republican Party. About February 1861two months before the war startedGray lost part of his left thumb, just above the base of the nail, in an accident in the garden. Despite now being 50 years old, he regretted that this accident ended his "fighting days." After hostilities began, he joined a company that guarded the Massachusetts State Arsenal in Cambridge. He also bought war bonds, was surprised more people did not do likewise, and supported a 5%tax to support the war. Gray regretted not having children because he had "no son to send to the war". Gray considered Abraham Lincoln as a second George Washington because of the way he managed to preserve the Union during the war. He also predicted that the fate of slavery depended upon the length and bitterness of the war, and the longer it lasted the more disastrous it would be for the South. As a corollary, he felt that if the South had given up early in the war, they would have had a chance of preserving slavery longer. Regarding his botanical endeavors, the war sundered his supply of information and specimens from the South. Even the Southern botanists who supported the North, such as Alvan Wentworth Chapman and Thomas Minott Peters, were soon forced to cease communications with Gray. It was during the war that Gray first began to think of retiring from his professorial duties so he could concentrate on completing "Flora of North America".