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The original circa 1882 depot was built by the P&A Railroad and burned around 1907. This present structure was built on the site of the original depot in 1909 by the L&N Railroad. It was built to their standard plans for a mid-size combination freight and passenger station. It was modernized in 1917 with the addition of indoor restrooms, an enlarged general waiting room, concrete platform, and a train shed over the new platform. The station was closed in 1973. Shortly after that the Santa Rosa Historical Society was formed to purchase the depot from the L&N Railroad. The society did a preliminary restoration as a 1976 Bicentennial project. The building was placed on the National Register of Historic Places in 1982. The West Florida Railroad Museum began operation in the depot in 1989 and did a major restoration of the building in 1992 upon receipt of a grant from the State of Florida's Bureau of Historic Preservation.