The Madrean Pine-Oak Woodlands Hotspot includes Mexico's main mountain chains, namely the Sierra Madre Occidental, the Sierra Madre Oriental, the Trans-Mexican Volcanic Belt, the Sierra Madre del Sur, and the Sierra Norte de Oaxaca, as well as isolated mountaintop islands in Baja California (particularly around the Sierra de la Laguna). Although the vast majority of the hotspot’s 461,265 km² lie within Mexico, a few scattered patches occur in the southern United States (represented by the Madrean Sky Islands, a series of about 40 mountain-tops in southern Arizona and New Mexico).

The complex geological history of the Madrean Pine-Oak Woodlands is evidenced by its rugged mountainous terrain, high relief and deep canyons. The Trans-Mexican Volcanic Belt, which runs from west to east across central Mexico, and serves as a bridge connecting the Sierra Madre Occidental and the Sierra Madre Oriental.

The climate of the hotspot is primarily temperate, with annual precipitation varying between 500 and 2,500 millimeters. Pine and oak forests are the characteristic vegetation type in the hotspot.