Abstract: A population with 133 F7 recombinant inbred lines (RIL) derived from the cross of “Yueyan 98”ד118-3” and a natural population with 94 tobacco accessions were used as materials, and joint linkage and linkage disequilibrium (LD) mapping analysis for tobacco bacterial wilt (TBW) resistance was carried out by using 253 SSR and 293 InDel markers. Four QTLs with 12%-30.10% of the explanation rate were detected by linkage analysis of the RIL population in four environments; and 8 haplotypes were found to be closely related to TBW resistance in three environments and explained 8.78%-11.42% of phenotypic variation by LD mapping with natural population. The integrated linkage-LD mapping of the RIL and natural populations was carried out and 8 haplotypes were detected to be closely associated with TBW resistance and explained 4.95%-6.93% of phenotypic variation. Four haplotypes were found to be associated with TBW resistance in at least two of the three analytical methods, two (Hap227 and Hap370) of them are with positive phenotypic effect, and the other two (Hap289, Hap368) are with negative effect. The results indicate that the strategy of joint linkage-LD mapping could accurately detect QTLs related to TBW resistance, and these haplotypes could provide reference for TBW resistance research and screening of TBW resistance materials.