The Sawtooth Wilderness encompasses the Sawtooth Mountains, which are part of the Rocky Mountains. The Sawtooth Mountains have at least 50 peaks over high, including Thompson Peak, the highest point in the range and the wilderness at . The second highest point in Mount Cramer. The northern Sawtooth Mountains formed from the Eocene Sawtooth batholith, while south of Alturas Lake the Sawtooth Mountains formed from the Cretaceous granodiorite of the Idaho Batholith.