The island's name is derived from the Bahamian pine (Pinus caribaea var. bahamensis), which was once a common species on the island. However, the pine population on the island has been devastated by several hurricanes, including Hurricane Donna in 1960 and Hurricane Andrew in 1992. As a result, the island is now home to mostly pine stumps, and the few remaining pine trees are often stunted or diseased.

Despite the loss of its namesake trees, the island still retains its name, Big Pine Key. This is likely due to the fact that the island is still known for its history of pine logging and its association with the pine industry, even though the pines are no longer a major presence on the island.