Seagrass beds are highly productive and important ecosystems, which can be found throughout the world. They are rated as the 3rd most valuable ecosystem globally (on a per hectare basis) -only preceded by estuaries and wetlands-, providing living space for a large number of organisms, including commercial and recreational fish species. Such organisms use this valuable habitat as a nursery ground and as shelter, in order to minimize the risk of predation, before migrating to the coral reef or the open sea. Other animals, such as dugongs or green turtles feed in the seagrass meadows, which not only act as an important sink for nutrients but also help to protect the coastline from erosion. Because seagrass have such important functions and values and due to their sensitivity to changes in water quality and their environment, they have become recognized as significant indicator species to reflect the general health of a coastal ecosystem, hence attracting considerable research interests. Here, the functions and ecological values of this ecosystem will be presented in more detail, with particular attention given to the threats that both man and nature pose to these unique ecological structures.