The seagrasses, a unique aquatic plants, are the most important component in the environmental food chain of the coastal ecosystems. The P.oceanica seagrass is an endemic for the Mediterranean region, and a main species in the marine coastal environment of Greece. Meadows of P.oceanica are subjected to the human activities, since they occur in coastal areas, where they are affected both by anthropogenic and by natural (climatic and environmental) factors. Nowadays P.oceanica is in the alarming state of regression, because of the deterioration of the environment in the Mediterranean Sea. Current work focuses on the methods of monitoring and mapping of P.oceanica along the northern coasts of Crete Island, Greece, and investigates the application of the remote sensing techniques for the seagrass mapping. Particularly, the optical properties of the P.oceanica and carbonate sand are reviewed and compared, in order to study distinguishability of various seafloor cover types with varying environmental conditions. The thesis provides contribution to the saving and protecting the environment of Mediterranean region.