The government had greater success in subduing another Athapaskan people, the Diné, or Navajos. Like the Apaches, the Diné ran off cattle, horses, and sheep from New Mexican settlements in the upper Rio Grande Valley. Lieutenant W.H. Emory of the Army of the West called them "lords of New Mexico" because they attacked communities from Zuni to Santa Fe. Unlike the Apaches, the Navajos used stolen animals to replenish their own herds. According to Charles Bent, the first American governor of New Mexico, the tribe possessed an estimated 30,000 horned cattles, 500,000 sheep, and 10,000 horses, mules, and donkeys. Those herds enabled them to spread across a vast region that stretched from the Chama River to the Little Colorado.
The Diné also cultivated more intensely than the Apaches, raising wheat, corn, beans, squash, melons, and peaches, especially in Canyon de Chelly. Anglo American observers emphasized Navajo raiding because raiding fit their preconceptions of Indian savagery, but the Navajo economy and Navajo-New Mexican relationships were far more complex. Both groups preyed upon each other, the Navajos rounding up new Mexican herds, the New Mexicans rounding up Navajos as slaves. They also traded with another, with the Navajos trading woolen blankets in return for silver, metal goods, and other commodities. Once the United States invaded New Mexico during the Mexican War, U.S. military authorities attempted to end the raids. Their policy puzzled the Diné, who thought that the Navajos and Americans were fighting a common foe.
For the next 17 years, U.S.-Navajo relations oscillated between conclusive peace negotiations and abortive military campaigns. Treaties were made at Jemez pueblo in 1852 and at Laguna Negra in 1855, but neither brought lasting peace. In 1858 a campaign led by Colonel Duixom Miles tried to track down Navajo war leader Manuelito. Two years later, Manuelito retaliated and nearly overturned Fort Defiance, established in 1851.
By the fall of 1860, the citizens of New Mexico were ready to take matters into their own hands. Five companies of volunteer milita commanded by Manuel Chaves scoured the Navajo country, killing any men they found and enslaving about 100 women and children. The volunteers also destroyed Navajo cornfields and captured thousands of cattle, horses, and sheep. In October 1862, Brigadier General James Carleton took command of the military department of New Mexico after leading his California Column across the Mojave Desert and Arizona. Carleton craved battle with the Confederates, whom he considered vile secessionists. By the time he arrived in Santa Fe, his predecessor, General Edward Canby, had already run the Confederates out of New Mexico. Carleton therefore turned his moral wrath on the Navajos and the Mescalero Apaches. Canby advised him that the only way to deal with the Apaches and Navajos was to force them onto remote reservations, and Carleton decided on a wide stretch of floodplain along the Pecos River known as Bosque Redondo.
Carleton chose Christopher "Kit" Carson, a beaver trapper, buffalo hunter, army scout, and Taos pioneer, to carry out his plans. Carleton commanded him to deliver an ultimatum to the Navajos. "Say to them: 'Go to the Bosque Redondo, or we will pursue and destroy you. We will not make peace with you on any other terms.'" In July 1863 Carson reached Fort Defiance, which he renamed Fort Canby, with more than 700 soldiers and Ute Indian scouts. The Utes tracked down the Navajos, killed the men, and seized the women and children as slaves. The soldiers burned Navajo cornfields, slaughtered their sheep, and confiscated their cattle and horses. As time went on, small groups of starving Navajos straggled into Fort Canby to surrender. By the end of the year, the only refuge left was Canyon de Chelly.
Carleton's forces entered Canyon de Chelly from the east and west. Carson fought no pitched battles with the Diné, but he once again systematically razed their fields and destroyed their herds. By February, hundreds of Navajos had embarked upon their Long Walk to the desolate Bosque Redondo, famished, freezing, and driven into exile. Carleton reported that Bosque Redondo held 8,354 of them by January 1865. Navajo independence had disappeared.