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Background:Tuberculosis (TB),caused by Mycobacterium tuberculosis complex (MTBC),is one of the major causes of death in the world today.Although China has the second largest global case rate of tuberculosis,a systematic study of TB prevalence in China has not been completed.From 2006 to 2007,the base line surveillance of tuberculosis was carried out by Ministry of Health,and more than 4000 representative strains were selected from 31 provinces in China.Methodology/Principal Findings:The aim of the present research was to survey the genotypes of representative Mycobacterium tuberculosis (M.tuberculosis) strains from China using spacer oligonucleotide typing (spoligotyping),and to analyze the relationship between genotype and drug resistance for the first time.A total of 4017 dinical isolates were collected from 2007 to 2008 throughout China.Among those M.tuberculosis isolates,2500 (62.2%) isolates were Beijing genotypes.The percentage of Beijing genotypes in northern China was higher than in southern China (76.5% vs.53.2%).Additionally,the frequencies of rifampin-resistant,ofloxacin-resistant and multidrug-resistant isolates were significantly higher in Beijing genotype strains than non-Beijing strains.Furthermore,a novel genotype named "Chna Southern genotype (CS)" was only isolated from Fujian and Guangdong provinces.Hence,it is very practical to uncover the reason for prevalence of the CS type in southern China.Conclusions/Significance:In conclusion Beijing family genotypes were still the predominant genotype throughout China,which exhibited a greater correlation with rifampin-resistance,ofloxacin-resistance and MDR phenotypes than other TB spoligotypes,and some regions of China showed severa un que characters in the distribution of M.tuberculosis genotypes.Our research represents an important contribution for the TB control and research community,which completes broad pictures on drug resistance levels and distribution of M.tuberculosis strain types over China.