San José Ayuquila is a town and municipality in Oaxaca in south-western Mexico.

The municipality covers an area of 35.72 km2.

It is part of the Huajuapan District in the north of the Mixteca Region.

As of 2005, the municipality had a total population of 1,342.

This article about a location in the Mexican state of Oaxaca is a stub.