Abstract: In order to find out the molecular markers related to tobacco bacterial wilt(TBW) resistance and speed up the breeding process of cultivars resistant to TBW,78 tobacco accessions were selected as natural population,genotyping was performed with 20 pairs of simple sequence repeat(SSR) primers and 37 pairs of microsatellite-anchored fragment length polymorphism(MFLP) primers.Principal component analysis and population structure analysis were conducted with allelic variation data,and the linkage disequilibrium association analysis between TBW resistance and allelic variants was carried out by TASSEL3.0 software.The results showed that 252 allelic variants were detected by SSR and MFLP in 78 tobacco accessions,these accessions were classified into 5 groups by both principal component analysis and population structure analysis.Association analysis indicated that 6 MFLP loci significantly associated with TBW resistance,which explained 8.33%-19.49% of the phenotypic variation of TBW resistance.These molecular markers can be used as reference indexes for evaluating the tobacco accessions with potential TBW resistance.