All Piman-speaking people probably originated near the present Arizona-Sonora border. After the Pima Bajo had moved south, an intrusion of the Opata and, later, other groups such as the Apaches, split the Upper from the Lower Pima. Spanish explorers visited the Pima in the lower reaches of the Río Yaqui in 1533 and took slaves. The early main route to the north, pioneered by Alvar Núñez Cabeza de Vaca's retreat from the Texas Gulf (1536), passed through Pima Bajo and Opata country, up the Sonora and other rivers into the Sierra Madre. Some explorers using this route included Marcos de Niza (1539), Francisco Vásquez de Coronado (1540), and Francisco de Ibarra (1565). Spanish miners penetrated the region of the upper Río Sonora in search of minerals in the late sixteenth century, but missionaries and settlers had a greater impact on the Pima Bajo in the seventeenth.
Jesuit priests contacted the first Pima in the lower Río Sinaloa in 1591 and established missions. Father Eusebio Francisco Kino arrived in the region in 1697, and soon thereafter Jesuits established a system of missions among the Pima Alto, protected by a line of presidios. The Franciscans worked with the Opata to the north. Except when the Pima rebelled against the Spaniards with the neighboring Tarahumara in 1697, with the Yaqui and Mayo in 1740, and with the Seri in 1751, the relationship between priests and Indians was largely peaceful, although paternalistic and exploitative.
During this period of early exploration and Spanish settlement, the Mountain Pima accepted elements of western European culture—particularly social and political organization, agricultural products and technology, and Catholicism. At the same time, the Jesuits tried to administer the Pima Bajo more effectively by gathering them into centrally located villages, where they could be converted and taught the principles of Christianity as well as Spanish social and political customs. This process was called reducción. Many Pima preferred their traditional ranchería life-style, which gave them freedom and arable lands for agriculture. The little resettlement that did occur was mitigated by a high death rate from diseases contracted through closer contact with Europeans. At this time, the Pima worked both Jesuit farmlands and Spanish mines, as well as their own farms. Sometimes mine officials removed Pima from the mission without consulting the missionaries and made the Pima work for goods and clothing assessed at inordinately higher prices, creating a form of debt peonage. In addition, Spanish settlers invaded Indian property for more land for cattle grazing.
In 1767 the Jesuits were expelled from the New World by order of the king of Spain. The Jesuits had faced conflicts with cattlemen and miners and had been unable to maintain the production of food and livestock because of constant attacks by raiding Seri and unrest among the Pima Bajo, particularly those in Névome country. After a brief hiatus following the Jesuits' departure, Franciscans replaced them and enlarged the mission fields and herds. Apache raiding after the early 1700s reduced mining activity and forced the Spaniards out of Pima Bajo territory by the end of the century. At first, the attacks were only against small groups of Pima caught unawares while cultivating or traveling. Residents of outlying ranchos moved into Maycoba for protection and only returned to their fields under armed escort. Even Yécora lay ruined and deserted in the 1790s. At one point, the Maycoba Pima purchased the church santos (statues of patron saints) from the Spanish to help them defeat the Apache. Raids increased after the mid-1850s as pressures from U.S. cavalry troops made life difficult for the Apache in the north.
After the 1910 Revolutionary War, according to Pima accounts, the new Mexican government acknowledged the help of the Pima in Maycoba in combating the Apache raiders by presenting them with ejido land. The war led to a large migration of Mexicans into northern Sonora, especially in the 1930s; these migrants took over Pima lands and watering places. Some Pima Bajo, such as those in Yécora and Sahuaripa, migrated into deeper recesses in the Sierra Madre rather than face open conflict. Like many of the Sierra Indian groups, the Pima Bajo have been gradually displaced by non-Indians and absorbed into the larger Mexican society. Ceremonial rituals and other cultural practices are more intensely observed by the highland than by lowland groups, and there is more separation—and conflict—between highland Pima and neighboring town-dwelling mestizos than is the case with the lowland groups.