Vegetation in Mount Jefferson Wilderness is predominantly Douglas-fir, Pacific silver fir, sub-alpine fir, mountain hemlock, lodgepole pine, ponderosa pine, several species of false cedars including, Alaska-cedar, incense cedar, and western redcedar as well as species such as vine maple, huckleberry and rhododendron. Lupine, red paintbrush, bear grass, and various species of lily are also common in the wilderness.