Abstract： Objective To comprehensively identify compensatory mutations in rpoA,rpoB and rpoC genes of rifampicin-resistant Mycobacterium tuberculosis (RIF-r MTB) and to evaluate the effect of rifampicin-resistant mutation type and lineage background on occurrence of compensatory mutations.Methods Published MTB whole genome sequencing data were searched and downloaded.RIF-r MTB was identified through known rifampicin-resistant mutations.Based on parallel evolutionary patterns,we identified putative compensatory mutations in the phylogenetic tree and calculated proportions of accumulating compensatory mutations in each rifampicin-resistant mutations' type and lineage background of RIF-r MTB.Statistic significance was analyzed by chi-square test.Results A total of 8 453 global MTB whole genome sequencing data were downloaded form ENA (covering 12 countries),including 1 749 RIF-r MTB.Based on phylogenetic analysis,we totally identified 60 putative compensatory mutations (6 in rpoA gene,16 in rpoB gene and 38 in rpoC gene),11 of which were newly reported.RIF-R strains carrying rpoB S450L (41.7％,279/669) had a significant higher chance to accumulate compensatory mutations than strains with other rpoB mutations (8.0％,31/388,x2 =378.5,P ＜ 0.000 1).In addition,RIF-R strains from lineage 2 (34.0％,223/656) had a significant higher chance to accumulate compensatory mutations than strains from other lineages [lineage1:4.7％ (2/43),2/43,lineage3:12.5％ (4/32),4/32,lineage4:15.1％ (78/517),78/517;x2 =238.5,P ＜ 0.000 1].Conclusions Our study comprehensively identified putative rifampicin-resistant compensatory mutations of rifampicin resistance.RIF-R strains carrying rpoB S450L mutation or from lineage 2 had a significantly higher chance to accumulate compensatory mutations than strains either with other rpoB mutations or from other lineages.