|Scleractinian corals harbor eukaryotic and prokaryotic organisms that form dynamic mutualistic, parasitic and commensal associations with the coral host and exhibit substantial genetic and ecological diversity. The microorganisms that inhabit the surface mucosal layer, tissues, and calcium carbonate skeleton of corals may provide the first line of defense against microbial infection, and evidence suggests that they play an intrinsic role in host fitness and disease susceptibility. Protection may be provided through the production of potent antibiotics or by filling an otherwise available niche open to infection by opportunistic pathogens. As corals are increasingly affected by catastrophic epizootics and bleaching events, it becomes increasingly important to understand the composition of coral-microbial assemblages and what causes the shift from a healthy to a diseased state. Often we correlate disease stressors such as high water temperature, sedimentation, nutrient loading, and overfishing, all of which may inhibit a corals innate ability to mediate an optimal microbial assemblage. However, as corals succumb to an early death there is an increase in colonizable substratum, which has provided an ideal environment for the proliferation of macroalgae, sponges, and other competitive dominants under present-day conditions. Coral-associated microbiota may be severely affected by the physical encroachment and allelochemicals exuded by encroaching organisms. This dissertation examines what is generally known about coral-microbial associations, briefly touching on coral disease and coral-algal interactions, followed by a laboratory assay that examines the allelochemical activity of common macroalgal extracts on coral reef microorganisms (Chapter 2). Additionally, I describe the species-specificity and geographic continuity of microbial assemblages associated with two common Caribbean coral species, Montastraea faveolata and Porites astreoides, in Belize, Florida, and St. Thomas (Chapter 3). Finally, I specifically examine the effect of encroaching macroalage and their allelochemicals on coral microbiota (Chapters 4 & 5). Better understanding of healthy coral-microbial associations and the ability of competing benthic organisms to physically or chemically shift these assemblages is critical to predicting reef resilience and the future of coral reef health.