We determined the role of endophytic bacteria of C. equietifolia, involved in synthesis of allelochemicals. The root endophytic bacteria were isolated and their biological activity was studied to determine their allelopathic potential in fermentation broth. Twenty one species of endophytic bacteria were isolated from the C. equisetifolia roots, of which Bacillus were the dominant genus, Acinetobacter and Staphylococcus were other dominant genera. These 21 endophytic bacteria inhibited the seeds germination of C. equisetifolia, among which Bacillus amyloliquefaciens was most inhibitory. Main allelopathic components of fermentation broth of 3-endophytic bacteria (Bacillus amyloliquefaciens, Bacillus aryabhattai and Paenibacillus glycanilyticus) with strongest allelopathic potential were rich in phenols, esters, organic acids, aldehydes, alcohols, ketones etc. Among them, two allelopathic substances [2,2'-methylenebis[6-(1,1-dimethylethyl)-4-methyl-Phenol and 1,2,3,4-Butanetetrol] were present in both endophytic bacteria fermentation broth and in root and soil extracts. These results confirmed that the secondary metabolites of C. equisetifolia root endophytic bacteria were allelopathic.