The invention belongs to the technical field of medicines, and relates to an engineering bacterium producing gentamicin A and an application thereof. The engineering bacterium is micromonospora purpurea (Micromonospora purpurea) KD1989 with a geneD1 inactivating function, which is registered and collected in China General Microbiological Culture Collection Center (CGMCC) with the collection No. CGMCC No. 8598. The genD1 function in gentamicin biosynthetic gene cluster is inactivated through a gene knockout method, and according to the gene knockout method, shuttle plasmids (such as pGD14 plasmid) are built and knocked out, the pGD14 plasmid is transformed into a gentamicin producing strain, double crossover engineering bacterium micromonospora purpurea GKD1989(delta genK+delta genD1) is screened, the engineering bacterium is fermented, and gentamicin A is determined by detection of metabolites. The engineering bacterium producing gentamicin A produces the single component gentamicin A, which has not been reported in China and foreign countries, so that the industrial production of gentamicin A can be realized; and the production process is simple and easily controlled, the extraction is convenient, the cost is low, and the engineering bacterium meets clean production levels, has stable product quality, and is the first innovative product in the world.