Marine and estuarine seagrass communities are ecologically and economically important intertidal and shallow subtidal communities. These highly productive and complex habitats range from cold temperate areas to the tropics, and from soft sediment environments to rocky shores. The approximately sixty seagrass species that form the basis of seagrass communities are angiosperms that produce diverse bioactive natural products, including phenolic compounds, steroids, terpenes, glycosides, sulfated polysaccharides, pectins, glycolipids, triglycerols, fatty acids, and volatile compounds. Of these, only phenolic compounds, which include phenolic acids, flavones, condensed tannins, and lignins, are well studied in terms of their production and ecological functions. Phenolic concentrations vary within and among individual plants as well as temporally. Differences in phenolic concentrations correlate with the developmental stages of leaves and environmental factors such as seawater pH, nutrients, light, salinity, and grazer damage. Seagrass natural products, including phenolic compounds, can deter herbivore feeding, inhibit the growth of pathogens and fouling organisms, and act as antioxidants. In addition to directly producing bioactive natural products, seagrasses can harbor organisms that synthesize and utilize them. Thus, the natural products produced by seagrasses and organisms associated with them play important roles in mediating ecological interactions among the organisms inhabiting these highly productive communities.