Research has highlighted the conserved and species-specific nature of coral-associated bacterial communities, however little is known about their interactions and ecological roles. With increases in coral disease correlating with climate change and the proposal that driving forces include compromised natural bacterial communities and increased pathogenicity of specific microbes, it is essential to understand how climate change is affecting the role of these communities in the coral ecosystem. Bacteria exploit elaborate inter- and intra-species communication systems to facilitate and regulate group behavior. Using small, diffusible signal molecules, bacteria regulate processes including biofilm formation, motility and the production of virulence factors, such as antibiotics on a population level; processes expected to have significant roles in the maintenance of bacterial communities within the coral niche. To investigate whether environmental change disrupts this communication network and thus microbial communities, methodology was developed to detect bacterial signal molecules within coral species in situ. Work with the Red Sea scleractinian Stylophora pistillata showed changes to the conserved bacterial communication profiles during temperature stress for the first time, indicating a possible link between climate change and bacterial communication. Further studies with the gorgonian coral, Eunicella verrucosa, from the SW English coast established the presence of spatially and temporally conserved bacterial populations associated with E. verrucosa tissue that are disrupted in a state of disease. Isolation of bacteria from E. verrucosa tissue has provided interesting studies of bacterial interactions with some changes to bacterial communication profiles found with temperature, nutrient and CO2 stress.