[Background] Microbial natural products have become an important source of small molecule drugs and prodrugs in recent years. Genomic analysis shows that Streptomyces antibioticus NRRL 8167 contains a variety of biosynthetic gene clusters of natural products, with the potential to generate multiple new compounds. [Objective] Study on the secondary metabolites in S. antibioticus NRRL 8167 to discover compounds with novel structures or unique biological activities, and further explore the corresponding biosynthetic gene clusters. [Methods] Using HPLC-MS and UV spectrum, we excluded the known compounds produced by S. antibioticus NRRL 8167 and identified an unknown compound with special UV-vis absorption as isolation targets. The secondary metabolites were isolated and purified using normal or reverse phase column chromatography and high-performance liquid chromatography (HPLC). The structures of the compounds were elucidated by using mass spectroscopy (MS) and nuclear magnetic resonance (NMR). The genomic DNA of S. antibioticus NRRL 8167 was extracted for genome sequencing by the PacBio sequencing platform. Bioinformatics technique was used to annotate the genome, to define the gene clusters that is responsible for the compound biosynthesis, and to propose its biosynthetic pathway. [Results] The compound was purified and identified as naphthgeranine A, belonging to polyketides. The whole genome sequence contains 28 secondary metabolites biosynthetic gene clusters. The gene cluster 20 is proposed to be responsible for the biosynthesis of naphthgeranine A. We also speculated the biosynthetic pathway of naphthgeranine A. [Conclusion] Naphthgeranine A was purified from S. antibioticus NRRL 8167 and structurally elucidated based on the UV-vis spectra, MS data and NMR. Complete genome sequence of this strain provided the opportunity for defining the gene clusters of naphthgeranine A. The proposed biosynthetic gene cluster and biosynthetic pathways laid the foundation for further research on the biosynthetic mechanisms of naphthgeranine A.