The museum is housed in a 1936 replica, built on a new site, of Don Antonio Gil Y'Barbo's stone house. Y'Barbo, founder of Nacog-doches, built the original stone house circa 1779 as the formal portal to the Spanish District of Texas. The original site of the house, torn down in 1902, is at the corner of Fredonia and Main sts. downtown.

During its history, the original house served as a public building, grocery store, candy store, and saloon, and as a temporary fortification during the Magee-Gutierrez, Dr. James Long and Fredonia Rebellion filibusters. In 1936, the same stones were in turn used to build the present structure on the campus of Stephen F. Austin Univ. The important landmark contains a continuing exhibit on the history of the house and temporary exhibits. Guided tours by reservation only.