Custer National Forest is located primarily in the south central part of the U.S. state of Montana but also has separate sections in northwestern South Dakota. With a total area of 1,188,130 acres (4,808 km2), the forest comprises over 10 separate sections. While in the westernmost sections, Custer National Forest is a part of the Greater Yellowstone Ecosystem, the easternmost sections are a combination of forest "islands" and grasslands. A portion of the forest is also part of the Absaroka-Beartooth Wilderness and constitutes over a third of the wilderness land. South of Red Lodge, Montana, the Beartooth Highway passes through the forest en route to Yellowstone National Park.

The Greater Yellowstone Ecosystem (GYE) is one of the last remaining large, nearly intact ecosystems in the northern temperate zone of the Earth. It is located within the northern Rocky Mountains, in areas of northwestern Wyoming, southwestern Montana, and eastern Idaho, and is about 22 million acres (89,000 km2). Yellowstone National Park and the Yellowstone Caldera 'hotspot' are within it.