As settlers began populating Montana from the 1850s through the 1870s, disputes with Native Americans ensued, primarily over land ownership and control. In 1855, Washington Territorial Governor Isaac Stevens negotiated the Hellgate treaty between the United States government and the Salish, Pend d'Oreille, and Kootenai people of western Montana, which established boundaries for the tribal nations. The treaty was ratified in 1859. While the treaty established what later became the Flathead Indian Reservation, trouble with interpreters and confusion over the terms of the treaty led Whites to believe the Bitterroot Valley was opened to settlement, but the tribal nations disputed those provisions. The Salish remained in the Bitterroot Valley until 1891.
The first U.S. Army post established in Montana was Camp Cooke in 1866, on the Missouri River, to protect steamboat traffic going to Fort Benton. More than a dozen additional military outposts were established in the state. Pressure over land ownership and control increased due to discoveries of gold in various parts of Montana and surrounding states. Major battles occurred in Montana during Red Cloud's War, the Great Sioux War of 1876, and the Nez Perce War and in conflicts with Piegan Blackfeet. The most notable were the Marias Massacre (1870), Battle of the Little Bighorn (1876), Battle of the Big Hole (1877), and Battle of Bear Paw (1877). The last recorded conflict in Montana between the U.S. Army and Native Americans occurred in 1887 during the Battle of Crow Agency in the Big Horn country. Indian survivors who had signed treaties were generally required to move onto reservations.
Chief Joseph and Col. John Gibbon met again on the Big Hole Battlefield site in 1889. Simultaneously with these conflicts, bison, a keystone species and the primary protein source that Native people had survived on for centuries, were being destroyed. Some estimates say more than 13 million bison were in Montana in 1870. In 1875, General Philip Sheridan pleaded to a joint session of Congress to authorize the slaughtering of herds to deprive the Indians of their source of food. By 1884, commercial hunting had brought bison to the verge of extinction; only about 325 bison remained in the entire United States.