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