The Middle Rockies Ecoregion is characterized by steep, high-elevation mountain ranges and intermountain valleys. This ecoregion is a disjunct ecoregion composed of three distinct geographic areas: 1. the Greater Yellowstone area in northwest Wyoming, southwest Montana, and eastern Idaho; 2. the Bighorn Mountains in north-central Wyoming and south-central Montana; 3. and the Black Hills in western South Dakota and eastern Wyoming. This ecoregion covers approximately 34,900 square miles (90,180 square km), and its three distinct geographic sections are bordered by several other ecoregions.

The Yellowstone section (1) abuts the Montana Valley and Foothill Prairies and the Northern Rockies Ecoregions to the north, the Snake River Basin and the Central Basin and Range Ecoregions to the west, and the Wyoming Basin Ecoregion to the south and east. The Bighorn Mountains section (2) lies between the Wyoming Basin Ecoregion to the west and the Northwestern Great Plains Ecoregion to the east, and it abuts the Montana Valleys and Foothill Prairies Ecoregion to the north. The Black Hills section (3) is entirely surrounded by the Northwestern Great Plains Ecoregion.

The Continental Divide crosses into this ecoregion through the north of Montana, then along the Montana-Idaho border until it enters Wyoming and Yellowstone National park, where it traverses in a southeast direction and exits the park into the Teton Wildernes. Then the divide continue in a southward direction, then southeast again across the Wind River range, then over South Pass for a short distance until the divide leaves the South Rockies ecoregion and enters the Wyoming Basin ecoregion when it skirts around the Great Divide Basin.

On both sides of the divide, topographic relief causes local climate variability, particularly the effects of aspect, exposure to prevailing wind, thermal inversions, and rain-shadow effects, that are reflected in the wide variety of flora and fauna within the ecoregion.

The climate of the Middle Rockies ecoregion lacks the strong maritime influence found in the Northern Rockies (3F). Many mountain-fed, perennial streams occur and differentiate the intermontane valleys from the Northwest Great Plains (4C).

Mountains have Douglas-fir, subalpine fir, and Engelmann spruce forests, as well as some large alpine areas. Pacific tree species are not dominant and forests often have open canopies. Foothills are partly wooded or shrub and grass covered. Intermontane valleys are grass covered and/or shrub covered and contain a mosaic of terrestrial and aquatic fauna that is distinct from the nearby mountains.

Common land uses include: recreation, logging, mining, and summer livestock grazing.

The Rocky Mountain Ranges in southern Idaho include:

Albion Mountains

Aspen Range

Bannock Range

Bear River Range

Big Hole Mountains

Blackfoot Mountains

Black Pine Mountains

Boise Mountains

Caribou Range

Castle Rocks

Cedar Hills

Chesterfield Range

Deep Creek Mountain

Grays Range

Ninety Percent Range

North Hansel Mountains

Owyhee Mountains

Peale Mountains

Portneuf Range

Pruess Range

Samaria Mountains

South Hills

Sublet Mountains

Webster Range