The history of the indigenous peoples of Oaxaca goes back to around 10,000 BC, with the arrival of the first nomadic groups in the Central Valleys of Oaxaca. The first evidence of the domestication of corn in the Valley of Oaxaca dates from around 5,000 BC, while beans have been grown since between 4,000 and 3,000 BC. The cultivation of these crops brought a definitive transition from a nomadic and semi-nomadic life to a sedentary one.

Two great civilizations marked the pre-Columbian history of Oaxaca. The Zapotec civilization bloomed from 300 BC from its base in the area of Monte Albán. Around 1200 AD, the Mixteca civilization prevailed before facing attempts at domination by the Aztecs in the XVth century and beginning of XVIth.

After 1520, the Spaniards conquered the region of Oaxaca taking advantage of local rivalries. The people of the Sierras (mountain ranges), mainly Zapotecs and Mixtecs put up the greatest resistance. On the other hand, the indigenous peoples were decimated by diseases like smallpox. In the Mixteca region (western Oaxaca), the native population fell from 700,000 at the time of the conquest to 25,000 in 1700.

It was during the Colonial period that the governmental structures and cultural patterns that prevail in the indigenous communities nowadays were formed, blending pre-Hispanic customs with colonial ones. These cultures have shown a great versatility in adapting themselves and absorbing changes over the last five centuries. The lack of formal territorial limits among innumerable indigenous communities in the state of Oaxaca at that time continues to be one of the sources of the present agrarian conflict.