[Objective] The genA inactive mutant was constructed on the basis of Micromonospora purpurea G1008, and then the function of genA was studied by analyzing the secondary metabolites. [Methods] Plasmid pAB103 used for the genA in-frame deletion was constructed and transformed into Micromonospora purpurea G1008 by conjugation. Apramycin resistance and PCR amplification were used to confirm Micromonospora purpurea GA1048. [Results] Gentamicin A2, instead of gentamicin C complex, was accumulated in Micromonospora purpurea GA1048, comparing with Micromonospora purpurea G1008. [Conclusion] The inactivation of genA led to the changes of gentamicin biosynthesis flow, and genA might be responsible for the methylation at C-3″ of garosamine.