Many plant species thrive in the Sky Lakes Wilderness, including nearly two dozen tree species. These range from the Pacific yew and Engelmann spruce in the lowlands to the mountain hemlock and subalpine fir at the higher elevations. Shasta red fir dominates much of the wilderness, and lodgepole pine is common but is in its element in the Oregon Desert portion of the wilderness. Whitebark pine is an uncommon tree in the area but can be found high on the slopes of Mount McLoughlin and Devil's Peak. The forest's understory is dominated by species of huckleberry, manzanita, kinnikinnick, snowbrush, and heather.