The Payette National Forest is highly diverse botanically. Plant communities include grasslands, shrubs, and forests. The grass and shrub communities are dominated by Idaho fescue, bluebunch wheatgrass, stiff sagebrush, mountain big sagebrush, and bitterbrush. The forest communities are dominated by ponderosa pine, douglas fir, grand fir, and subalpine fir.

A variety of wildflowers and other vascular plants also grow on the Forest. Thirty-eight of these species are so rare that Forest Service biologists are tracking and protecting their habitat. Habitats for the threatened species, Macfarlane's four-o'clock, occurs in the Hell's Canyon area. Habitat for fifteen sensitive species of milkvetch, onion, camas, phlox, saxifrage, and monkeyflower occur from the grasslands of Weiser to the high, subalpine forests east of McCall.

From the canyon lands of the Snake and Salmon River to the alpine mountains and meadows near McCall and New Meadows, over 1,500 plants grow and bloom from early March until late September.