<jats:sec><jats:title>Background</jats:title><jats:p><jats:italic>Streptomyces</jats:italic>are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from<jats:italic>Streptomyces kebangsaanensis</jats:italic>, an endophyte isolated from the ethnomedicinal<jats:italic>Portulaca oleracea.</jats:italic></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of<jats:italic>S. kebangsaanensis</jats:italic>in producing other useful secondary metabolites.</jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The<jats:italic>S. kebangsaanensis</jats:italic>genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis.</jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of<jats:italic>S. kebangsaanensis</jats:italic>for producing various antibiotics and secondary metabolites.</jats:sec>