The Florida Keys National Marine Sanctuary is a U.S. National Marine Sanctuary in the Florida Keys. It includes the Florida Reef, the only barrier coral reef in North America and the third-largest coral barrier reef in the world. It also has extensive mangrove forest and seagrass fields. The marine sanctuary includes a 2,800 square nautical mile (9,600 km²) area surrounding the Keys and reaching into the Atlantic Ocean, Florida Bay and the Gulf of Mexico. The sanctuary was established in 1990.

Covering much of the ocean floor are beds of seagrass that are of vital importance to the coral reef ecosystem. It is the largest known seagrass bed in the world.

Coral reefs and other marine life in the Florida Keys National Marine sanctuary are threatened by human activities.

Population growth and urban development are some of the greatest threats to coral reefs. Development activities cause erosion, resulting in the run off of sediments that eventually reach the coral reefs. Storm water run-off carries fertilizers into the ocean, causing damage to the coral reefs. Increase of nutrient concentrations in the reef causes an increase of algae, which may smother the corals.

Along with human population growth, the harvest of resources from the sea is ever growing. Overfishing has changed the ecological dynamics of marine communities, allowing some organisms to dominate reefs, that were once controlled by large reef fish populations.
Fishing practices can be just as damaging to the reefs as population decrease.

The increase of tourism is responsible for the increase in reef damage. Divers and snorkelers may harm the corals by touching the polyps. Boats transporting tourists to the reef may damage it by dragging anchors.

Global climate change may increase the sea temperature and sea level as well as ocean currents patterns, which all can cause damage to reefs. Corals are very sensitive to water temperature changes; rises in temperature result in coral bleaching.