Background Currently,migration has become one of the risk factors of high burden of tuberculosis in China.This study was to explore the influence of mass migration on the dynamics of Mycobacterium (M.) tuberculosis in Beijing,the capital and an urban area of China.Methods Three hundred and thirty-six M.tuberculosis strains from the Changping district,where the problem of urban migrants was more pronounced than in other Beijing regions,were genotyped by Spoligotyping,large sequence polymorphisms (LSPs 105 and 181),and variable number tandem repeat (VNTR) typing.Based on the genotype data,the phylogeny of the isolates was studied.Results In Changping district,the proportion of Beijing lineage M.tuberculosis isolates amounted to 89.0％ (299/336),among which 86.6 ％ (252) belonged to the mod lineage.The frequency of mod Beijing lineage strains is so high (around 75％ (252/336)) that associated risk factors affecting the tuberculosis epidemic cannot be determined.The time to the most recent common ancestor (TMRCA) of the Beijing lineage strains was estimated to be 5073 (95％ CI:4000-6200) years.There was no significant difference in the genetic variation of Beijing isolates from urban migrants and local residents.Conclusions The clone of mod Beijing lineage M.tuberculosis,which is dominant in the Beijing area,most likely started to expand with the five thousand-year-old Chinese civilization.In the future,with the urbanization in the whole of China,mod Beijing lineage M.tuberculosis may gain the larger geographical spread.