The isolation of the endophytic bacteria from mangroves and screen of the antagonistic bacteria against the Phytophthora capsici were studied in this paper. The results showed that there were a large number of the endophytic bacteria in the tissues of mangroves. Of the endophytic bacteria, about 27.97% strains expressed the inhibitive activities to P. capsic. Using the eighteen antagonistic bacteria to control pepper fruit Phytophthora blight showed that all the tested strains had some control efficacy to the disease. In them, strain RS261 isolated from the leaf of Rhizophora stylosa was found to have the best control efficacy. Based on the morphological, physiological and biochemical characteristics and on 16SrDNA sequences analysis, strain RS261 was identified as Bacillus amyloliquefaciens.