Gentamicin and sisomicin are two different aminoglycoside antibiotics. The comparison of their chemical structure and biosynthetic gene clusters, coupled with bioinformatic analysis, suggested that the gntK gene would be associated with methylation. The gntK gene fragment in M. purpurea G1008 was inactivated by genetic engineering and its mutant strain M. purpurea GK1101 (ΔgntK) was screened. The metabolites of G1008 and GK1101 was analyzed by HPLC-MS, which revealed that GK1101 no longer produced gentamicin C(1) or C(2), while mainly synthesizing gentamicin C(1a), and the production of C(1a) increased significantly. This indicated that the metabolic flow for the gentamicin C(1) and C(2) biosynthesis was blocked by disrupting the gntK gene, which substantiated that the gntK gene encoded the enzyme that catalyzes the methylation of purpurosamine C-6'. The mutant GK1101 has good prospects for industrial application. In addition, our study provides information that can be used to clarify the function of a single gene and simplify the targeted genetic breeding of important pharmaceutical microorganisms.