On old Spanish charts, Pigeon Key was known as Cayo Paloma (dove or white pigeon). Many believe this 5.31-acre island located beneath the Old Seven Mile Bridge, just west of Marathon, was named after the white-crowned pigeon of the Florida Keys.

Nobody had much use for Pigeon Key until Henry Flagler needed it to complete the Seven Mile Bridge, which was part of the Florida East Coast Railroad . At that time, the bridge was known as "Knights Key-Pigeon Key-Moser Channel-Pacet Channel Bridge".

Work began on the island in the spring of 1909, and by the beginning of 1912, it held four bunkhouses, each designed to hold 64 men; an engineering/office building, which also held sleeping quarters for the men who worked there; and numerous tents set up over wooden floors on stilts for the laborers. Food was good and plentiful and strict cleanliness was the law.

Originally, the design for the portion of the Seven Mile Bridge in the Pigeon Key area called for it to be a rock-filled causeway, as the water in the area was shallow enough to build it that way. Of course, the final decision was to make the entire span a bridge.

When the railroad was completed all the way to Key West in 1912, Pigeon Key was transformed from a construction camp into a bridge tender maintenance camp. Some of the original buildings were replaced with more permanent structures, some of them homes. In an attempt to attract and keep more married personnel, a school was opened in 1923. A post office was established the same year and remained open for 10 years. After the Labor Day hurricane of 1935, Pigeon Key became the southern base for rescue, relief, and evacuation operations.

As a result of the damage to the Overseas Railroad caused by the 1935 hurricane, the railroad bridges were transformed to the roadbed for part of the new Overseas Highway . Pigeon Key was headquarters for the construction of this roadway, which was a toll road until 1954. After the tollbooths were dismantled, land title for Pigeon Key was transferred to Monroe County.

In 1960, Hurricane Donna damaged two of the buildings so much that it was decided to burn them down. A few years later, the University of Miami leased the land for a marine biology project. This lease was cancelled in 1987.

In 1992, the Pigeon Key Foundation was formed as a joint venture between the Monroe County Environmental Education Task Force and the Mote Marine Laboratory of Sarasota, Florida, and a 30-year lease was granted. Today, seven historic structures remain alongside a few more structures added over the years.

A multi-use educational and meeting facility is housed in the restored Section Gang's Quarters. PKF offices are located in the Assistant Paint Foreman's House. The Assistant Bridge Tender's House now serves as a museum dedicated to the railway and early highway history. The Bridge Worker's Dorm and Negro Quarters have been restored and are used as sleeping quarters. The rest of the historic buildings and the additional structures have all been restored.

The Pigeon Key Foundation, a non-profit organization, has transformed this island and its buildings into a world-class educational center; a place to teach visitors about the splendor of the cultural and natural resources of the Florida Keys, and a nationally recognized concert and event location.