While Henry Flagler was building the Oversea Railway to Key West in the early 1900s, more than 400 workers lived in the railroad village on Pigeon Key, located in the path of the Old Seven Mile Bridge. Pigeon Key had a post office, commissary and one-room school while the bridge was being built from 1908 to 1912.
When a hurricane destroyed the railway in 1925, Pigeon Key became the headquarters for the Florida Road and Toll Bridge District. Starting in 1968, the island served for 20 years as an environmental field station for international researchers studying tropical marine and island ecologies with the University of Miami. In 1993, the Pigeon Key Foundation assumed stewardship and began restoration efforts to turn it into a museum.
In 2017, Hurricane Irma caused substantial damage to the 1912 Commissary and the 1940 Honeymoon Cottage, knocking both structures off their foundations. Both buildings have been deemed repairable and will be fully restored in 2018.