Scleractinian coral are the major building organisms of tropical reefs. The changes in climate and increase of human impacts have negatively affected the growth and health of reefs around the world. This project studied the effects of local stressors on the microbial community of Sri Lankan coral reefs and investigates epigenetic processes occurring in select scleractinian coral cells. First, differences in both taxonomy and function of coral reef associated microbes on healthy and degraded reefs across the island nation of Sri Lanka were identified. Order Rhodobacterales dominated the taxonomy at nearly every site and genes associated with carbohydrate metabolism, specifically genes associated with oxidative decarboxylation, were positively correlated with benthic coral cover. This suggests that at sites with higher benthic coral cover, the microbial community is utilizing the most effective methods to extract energy from the available complex carbon sources. This is opposed to sites where more easily consumed liable carbon from algal sources is available and less efficient metabolisms are needed. In a second study, scleractinian coral tissue was dissociated from the calcium carbonate skeleton in order to identify epigenetic processes in select cell populations. After utilizing FACS to separate cell populations, a population of cells was identified with a lower percentage global DNA methylation. The difference in DNA methylation suggests variable DNA expression and regulation in different cell types. Changes in DNA methylation and regulation in response to environmental factors could lead to phenotypic plasticity in Scleractinian coral and provide a mechanism for rapid adaptation to changing environmental conditions. Leveraging the knowledge learned from these reef studies, reef restoration projects can start to encompass both microbial and epigenetic influences into successful reef restoration.