Production of thaxtomin A (TXT), a nitrated dipeptide which inhibits cellulose synthesis in expanding plant tissue, is regarded as the major pathogenicity determinant in Streptomyces scabies, the most widely studied pathogen causing scab disease in economically important crops such as potato. It is known that TXT biosynthetic genes txtA, txtB, txtC and their regulator txtR are clustered together on the pathogenicity island (PAI) of the genome of S. scabies and are conserved in TXT-producing Streptomyces spp. including S. scabies. Here we reported an efficient method to establish the knock-out mutant of txtB (txtBΔ), by using intergeneric conjugal transfer system constituting Escherichia coli ET12567 /pUZ8002, S. scabies and the vector pKC1139. Briefly, a txtB gene-specific deletion cassette was constructed by PCR and long multiple fusion (LMF), which was subcloned into the Streptomyces-E. coli shuttle vector pKC1139, generating pKC1139-x. By mixing the donor E.coli ET12567 /pUZ8002/ pKC1139-x and the recipient S. scabies at the suitable condition, the exconjugants were successfully obtained and verified by colony PCR. Subsequently, TXT was analyzed for the knock-out mutant (txtBΔ) in comparison to wild-type of S. scabies. In addition, the transcriptional levels of txtB were studied between the two genotypes. Altogether, txtB gene was successfully knocked out in the exconjugants obtained herein. This would lay a foundation for studying the TXT-biosynthesis associated genes and pathogenicity in scab-causing plant pathogen, facilitating the mechanistic elucidation of plantpathogen interactions.