Abstract:[Objective] Lomofungin is a phenazine antibiotic with broad-spectrum anti-bacterial activity and is biosynthesized by Streptomyces lomondensis. In the lomofungin producing strain, S. lomondensis S015, a methyltransferase gene lomo3 at the downstream of the phenazine biosynthesis core gene cluster was studied. [Methods] we inactivated lomo3 by in-frame partial deletion and obtained strain S015Δlomo3. Complementary strain S015Δlomo3::lomo3 was then constructed. To investigate the function of lomo3, we analyzed the metabolites in the fermentation broth of S015, S015Δlomo3 and S015Δlomo3::lomo3. [Results] Inactivation of lomo3 in S. lomondensis S015 resulted in the absence of lomofungin production. The lomo3 complementary strain S015Δlomo3::lomo3 regained the biosynthesis of lomofungin. [Conclusion] This methyltransferase gene lomo3 plays an important role in the biosynthesis of lomofungin. The information obtained in this study laid a theoretical foundation for the biosynthesis of lomofungin.