In seagrass beds, vagile epifauna plays a major role in the energy transfer from primary producers to higher trophic levels. The main aim of the work was to examine the relationship between the seagrass complexity and the vagile epifauna community structure, and to study the role of this compartment within the food web of Thalassia testudinum seagrass beds. Two seagrass sites were compared, one near the coastal mangrove and another one near the barrier reef, during two seasons. Trophic resources used by primary consumers were assessed by combining stable isotopes analysis and fatty acid compositions. The coastal seagrass bed is complex due to its long leaves and its great biomass of litter and epiphytes. It shelters a great abundance and diversity of Crustaceans. The feeding preference of them for micro-algae and detrital particles promotes biofilm contribution to food web of the coastal seagrass bed. The seagrass bed located seawards, lesser complex, harbors an Invertebrate community dominated by the Gastropods Cerithiidae. The reduced food availability in that seagrass bed explains the higher contribution of litter and Thalassia leaves to that food web compared to the coastal seagrass bed. By coupling stable isotopes and stomach contents analyses, it was possible to highlight the major role of shrimps in the feeding diet of fishes. The coastal seagrass bed, where the trophic resources are more abundant and diverse, better plays its role of nursery for juveniles fishes than the seaward seagrass bed.