The Jackson Hole Historical Society was not founded until 1965, seven years after the museum. They merged in 1989. Though they have separate buildings, both the museum and Historical Society are maintained by the same board members. Much of the research done by the Historical Society is beneficial to the museum.
The museum offers a series of programs focused on specific issues. The History of Conservation Series offers information about the conversation efforts in the neighboring national parks, Yellowstone and Grand Teton. Two of the other programs focus on Native American History and local history/outdoor recreation. Experts in these fields come to give lectures and hold book signings. The museum also has a Local Authors Series, acknowledging locals who have published work about their way of life in Jackson Hole. A large portion of the museum is dedicated to Native American appreciation. The museum had so many artifacts from native tribes, they opened a second location. Indians of the Greater Yellowstone museum is much smaller and just around the corner from the original. The second museum is essentially a large exhibit dedicated to the area's native tribes. According to history, the Yellowstone area served as both temporary and permanent homes to the Mountain Shoshone, Eastern Shoshone, Crow, Kiowa, Lakota, Cheyenne, Bannock, Nez Perce, Blackfeet, Flathead, Gros Ventre, Pend d'Oreille, and Kootenai tribes.
The museum has partnered with the Jackson Hole Archaeological Initiative and local Boy Scouts to support the continued exploration and preservation of the Greater Yellowstone Ecosystem. In the past, archaeologist have discovered frozen wicker baskets, Paleo-Indian dart points, and spears left thawing in ice patches. Areas of high elevation react differently to climate change, making the mountains of Yellowstone an archaeologist's playground. The discoveries made on during these research expeditions can be found within the museum's exhibits.