Macrozoobenthos is basic aquatic organism that live on the surface (Epifauna) or inside (Infauna) the basic substrate that lives sessile in coastal ecosystem in the form of mangrove, seagrass and coral reef ecosystems. Macrozoobenthos can be used as a biological parameter in determining water quality. The aim of the research is 1. Knowing the results of measurements of water quality parameters in each research location point 2. Knowing types of makrozoobenthos (epifauna) in seagrass, mangrove and coal reef ecosystems 3. Knowing the structure of the macrozoobenthos community. The data retrieval is done using purposive sampling method. Based on the results of observations, there were 15 types of 3 macrozoobenthos phylum, namely phylum of Mollusca, Echinodermata and Arthropoda. From the calculation of the community structure of macrozoobenthos in the mangrove ecosystem, the value of the diversity index (H') is low, the uniformity index (E) is moderate and the dominance index (C) is high. The seagrass ecosystem and coral reef have moderate (H') diversity values, high (E) uniformity index and low (C) dominance index.