Seagrasses are unique flowering plants that have evolved to live in seawater and belong to a group of plants known as angiosperms. Seagrass ecosystems that occur in tropical and subtropical shallow marine waters are ranked high amongst the Earth’s most productive ecosystem and therefore serve as a source of energy for complex food webs in shallow coastal waters (Duarte, 1991). They serve as a nursery, refugia, breeding ground and home to many marine fishes, reptiles, and invertebrates with important economic, ecological and conservation value (Thorhaug, 1986; Walker & McComb, 1992). They form an ecosystem, dominating it as a discrete functional, not as a taxonomic group (McKenzie et al., 2010). In the Philippines, 18 seagrass species from three families (Hartog & Kuo, 2006) have been found from the 529 sites visited (Fortes 2008, Fortes 2012). Seagrasses attached to all types of substrates occur mostly extensively on soft ones. They are commonly found in the intertidal region up to 30 meters in depth (Alimen et al., 2010). According to Waycott et al. (2009), seagrass meadows are important as nutrient cycling, magnitude enhancement of coral reef fish productivity, the habitat of fish and invertebrates species, and major source food of endangered species like the manatee and green sea turtle. Seagrass meadows are comparably important as mangrove and coral reef ecosystems. McManus et al. (1992) estimated some 20 MT of fish, seaweeds and invertebrates may be harvested per km2 – year in a seagrass bed. Here in the Philippines, seagrasses have significant importance to artisanal fishermen because of the rabbitfish fishery (Duray, 1990; Salita et al., 2003). Moreover, Vandeklift and Jacoby (2003) discussed the assemblage of fish changes when there is a grass loss. The change of fish assemblage in the system causes fish migration into a suitable environment and other fish to emigrate. The changes of the marine organisms during the loss are relative to the change in the diversity of the seagrass meadow. Dugong (Dugong dugon), for example, are specific to eat Thalassia hemprichii (main diet), Syringodium isoetifolium and Cymodocea spp., while green sea turtle (Chelonia mydas) are eaten Thalassia hemprichii and Enhalus acoroides (Andre et al., 2005). In Gigantes Islands, all seagrass areas in Gigantes Islands had been enacted by the Local Government Unit (LGU) of Carles as fish sanctuaries, however, a lot of local fisherfolks are still utilizing the area for shellfish gleaning, boat anchoring and fishing activities even that the fishery ordinance for prohibition in the sanctuaries is in placed. With these important values both in economic and ecological services of seagrass habitat, hence, this study was conducted. The objectives of this study were to determine the present status of the seagrass ecosystem in the islands, the diversity indices and will serve as baseline information for the LGU.