Corals, considered the rainforests of the oceans, harbour an abundance of different bacterial populations throughout the coral structure. In the present study we attempted to characterize the cultivable bacterial population associated within the mucus and tissue of the coral Acropora digitifera from the Gulf of Mannar. 16S rRNA gene was amplified from the cultured mucus and tissue isolates. Amplified ribosomal DNA restriction analysis, performed with a combination of restriction enzymes to determine the polymorphic groups of bacteria, generated 19 distinct groups in the coral mucus and 17 distinct groups in the coral tissue. Phylogenetic analyses based on the full-length sequences of 16S rRNA gene sequences showed that the majority of bacterial isolates belonged to the group Firmicutes, followed by Gammaproteobacteria and Actinobacteria. On investigating their antimicrobial activity, mucus isolates showed about 25% activity and tissue isolates showed 48% activity. This study revealed the presence of actinomycetes in both the coral mucus and the coral tissue, which had high activity against pathogens. This study, for the first time, demonstrates that actinomycetes existing within corals also have potential antibacterial activity. This has been overlooked so far, and indicates that, in addition to mucus, bacteria within the tissue of corals might defend the coral host against pathogens.