Coral reefs are structurally and ecologically complex ecosystems with high biodiversity of algae, invertebrates and fishes living on them. Scleractinian corals, along with a few species of calcareous green and red algae, are responsible for their formation, but the corals must compete for substrate dominance against faster growing fleshy algae and encrusting invertebrates. Healthy coral reefs are characterized by high coral cover and relatively low cover of fleshy algae and other organisms. High rates of grazing by herbivorous fishes and invertebrates moderate competitive interactions among benthic dwellers, and play a critical role in determining coral reef community structure. Benthic competitors also use secondary metabolites to compete for space and avoid predation.

Synergistic effects of global-warming-related temperature stress on corals and their endo-symbiotic algae, epidemics of diseases, over-fishing which affects community structure and trophic dynamics, degraded water quality and sedimentation stress, have resulted in world-wide decline of coral cover on coral reefs . With few herbivores remaining, dead coral skeletons and reef substrates are increasingly over-grown by macroalgae, and larval corals have a difficult time recruiting.

Coral reef research at UNCW is focused on basic and applied aspects of biology, physiology and ecology of reef corals and other reef biota. Several projects focus on the early life histories of reef corals, including the molecular mechanisms for establishment of the algal endosymbiosis, chemical cues that induce settlement, initiation of skeletogenesis, all with the goal of understanding physical and biological processes that are critical to recruitment success and coral reef recovery (Szmant laboratory). Chemical ecology of reef invertebrates, and the role secondary metabolites play in species interactions important to community structure is another area of strength at UNCW (Pawlik). Studies of biodiversity and molecular ecology of coral reef fishes and invertebrates are both basic and applied in nature in that they contribute to the understanding of the function of marine reserves (McCartney). Other areas of interest include nutrient cycling within reef systems and algal community dynamics (Szmant). Formal courses are offered in Coral Reef Ecology (Szmant) and Reef Fish Ecology (Clavijo).