A coral-associated bacterium was successfully screened for secondary metabolite production based on biological activity and PCR amplification of the non-ribosomal peptide synthetase (NRPS) gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of other coral-associated bacteria and pathogenic bacteria. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity), a multifunctional peptide synthetase from Nostoc sp. GSV224 and NdaB (44% identity), a peptide synthetase module of Nodularia spumigena. To estimate the possible role of secondary metabolites, analyses on the quantitative proportion of Pseudoalteromonas was carried out. The results revealed that Pseudoltermonas group was indeed present within surfaces of coral Acropora sp.