Abstract: In this study,two endophytic bacteria coded YK-7 and YK-10 with significant antimicrobial activities,were isolated from halophyte Salicornia bigelovii.Torr,and identified their genera status by morphological characters and molecular biology method coupled with the physiological and biochemical experiments,as well as predicted and verified their fermentation products.The results showed that the two strains were characterized as Bacillus amyloliquefaciens subsp.Plantarum and Bacillus aryabhattai,respectively.The strain YK-7 was found to contain the non-ribosomal peptide compounds synthetase( NRPS) gene fragment after the PCR amplification of NRPS gene.YK-7 had the capability to of produce cyclic-lipopeptide Surfactin by the analysis of NRPS phylogenetic tree. The result was further confirmed by the detection of its fermentation product using an electrospray ionization mass spectrometry( ESI-MS) analysis.This study highlights the advantage of phylogeny-guided pipeline for the screening of bioactive compound from gene type to chemical type by a predication procedure.