In 1836, a small group of Presbyterian missionaries traveled with the annual fur trapper's caravan into "Oregon Country." Among the group, Narcissa Whitman and Eliza Spalding became the first white women to travel across the continent. Differences in culture led to growing tensions between the native Cayuse people and the Whitmans. Their mission became an important stop along the Oregon Trail, and passing immigrants added to the tension. A measles outbreak in 1847 killed half the local Cayuse. Some of the Cayuse blamed these deaths on Dr. Whitman. Dr. and Mrs. Whitman were killed; sixty others were taken hostage. The deaths of the Whitmans shocked the country and prompted Congress to make Oregon a U.S. territory.
In more recent times, the site has been excavated for important artifacts, and then reburied. A memorial obelisk, erected fifty years after the event, stands on a nearby hill.
The was established in 1936 as Whitman National Monument and was redesignated a National Historic Site on January 1, 1963.