Minicoy lagoon harbours extensive beds of Thalassia hemprichii in association with Syringodium isoetifolium, Halophila ovalis and Halodule uninervis. The total area occupied by seagrass flat ranges from 2.0 to 2.2 sq.km. Net primary production (NPP) of seagrass species varied from 5.0 gC/m3/day (0.5 gC/kg (wet wt.)/day for Syringodium to 10 gC/m3/day (1.0 gC/kg (wet wt.)/day for Halodule. It was estimated that an impairement up to 50 % on the NPP of Thalassia plants was caused by the prolonged exposure of the beds to bright sunshine in the intertidal areas during ebb stage when compared to those Thalassia plants growing in the unexposed habitats. Wet biomass, density of seagrass species and their NPP potential on the community metabolism of the lagoon are discussed.