Seagrass beds support a great abundance and diversity of benthic organisms, providing important spawning, nursery, protection and food to fish and invertebrates. This study characterized the macrofauna associated with a seagrass meadow in Ensenada de Yapascua, Parque Nacional San Esteban. Four zones were selecting within, with two perpendicular transects to the coast, with five sampling points of 1 m, 10 m, and at the end of the bed (15–20 m). Samples were taken from the mouth to the internal of the inlet during the rainy season (July-November 2015). A marked zonation of the species Thalassia testudinum and Halophila stipulacea was observed. The biomass of T. testudinum was higher in July, especially near the mouth of the inlet (Z1 and Z2) and H. stipulacea in November. A clear separation was observed between Zones 1 and 2 where T. testudinum dominated, and zones 3 and 4, where the biomass of H. stipulacea was greater. The total density of benthic organisms was 13,800 ind/m2, the most representative were: polychaetes (30%), nematodes (19%) gastropods (18%), and peracarids (14%). In July, a higher density of organisms (17,340 ind/m2) was estimated (November 11,680 ind/m2), with more than 70% dissimilarity near the mouth of the inlet compared to zone 4 (internal). These variations could be attributed to greater standing biomass and density of T. testudinum in the mouth, which represent more resource availability and physical complexity. These results highlight the effects of the presence of that invasive species H. stipulacea
