In 1533, the Yaquis saw the first white men: a Spanish military expedition searching for slaves. The Spanish who initiated warfare were soundly defeated, but took thousands of Yaqui lives. Between 1608 and 1610 the Spanish repeatedly attacked the Yaqui people. The Yaquis proved they could raise a fighting force of 7,000 within a few hours to successfully defend Yaqui land and cultural integrity.
Nevertheless, the Yaquis preferred peace. They asked the Jesuits to enter Yaqui villages to do missionary work and economic development. Most of the 60,000 Yaquis settled into eight sacred towns or "pueblos" and built churches: La Navidad del Senor de Vikam, Santa Rosa de Vahkom, La Asuncion de Nuestra Senora de Rahum, Espiritu Santo (Ko'okoim), Santa Barbara de Wiivisim, San Ignacio de Torim, San Miguel de Veenem, and La Santisima Trinidad de Potam.
Silver was discovered in the Yaqui River Valley around 1684. The Spanish, who treasured the silver stone, began moving into the area, began taking sacred Yaqui land, and treated the Yaqui people disrespectfully.
In 1740, the Yaqui allied with the neighboring Mayo tribe to force the Spanish out of the God-given Indian lands. For the next 190 years, the Yaqui people continued to fight the Spanish, and then the Mexicans (after they won their independence from Spain).
Juan Banderas was one Yaqui leader who tried to unite the Mayo, Opata, and Pima tribes with the Yaqui tribe in attempt to force the Mexicans out of Indian country. He was caught with an Opata chief in 1833 and was executed.
By this time, the Yaqui people had suffered greatly. Many Yaquis left the Rio Yaqui area to fight in the Vakatetteve Mountains; others relocated to Yaqui communities in Arizona. Many more died in battles or were executed. In 1868, 600 Yaqui men, women, and children were captured near Vahkom Pueblo by Mexican state and federal troops. Their arms (bows and arrows and rifles) were taken, and 450 were locked in a church. During the night, the church was shelled. 120 of the people inside were massacred. But still, the Yaquis continued to believe in and fight for the right to land, autonomy, and freedom from harassment.