[2] The Patagonia Mountains begin near the Mexico border east of Nogales, Arizona.

Above and to the east of the basin lies the largest endemic stand of ponderosa and Chihuahua pines in the range.

The Sierra San Antonio are a continuation of the Patagonia Mountains southwards into Mexico, a mountain range of about 10 miles in length that tapers down to lower elevations where the Santa Cruz River makes its bend near the Sonoran town of San Lázaro.

The San Rafael Valley and Canelo Hills are to the east of the Patagonia Mountains.

The connected Santa Rita, Patagonia, and Sierra San Antonio ranges are part of the Madrean Sky Islands ecoregion, the sky island mountain ranges region on the north of the Sierra Madre Occidental, the major cordillera and mountain ecoregion of central-western and northwestern Mexico.