The museum opened in March 1981 in the historical center of La Paz, with the aim of preserving and exhibiting the cultural heritage of Southern Baja California. The museum building was constructed in the twentieth century by the architect José Figueroa Vázquez, and houses an extraordinary collection which ranges from the remote past of Baja California Sur up until the time when it became a free and sovereign state.

The objects, finds, explanations and works of art exhibited here reflect universal values, such as the cave paintings of the Sierra de San Francisco, which are a World Heritage Site. The space also reflects the world view of a people who were forged in a desert peninsula, far from the main centers of population in Mexico, endowing them with a unique culture that endures to this day. Within the permanent galleries, this singularity is reflected in the careful curating and the museum displays, as well as the outstanding and fascinating paleontological, archeological, ethnographic and historical collections.