Abstract: Objective To explore the characteristics of molecular epidemiology of multi-drug Mycobacterium tuberculosis clinical isolates in Fujian province,and to provide reference for multi-drug-resistant tuberculosis(MDR-TB) control.Methods All MDR-TB isolates were selected from 30 survey sites,and the bacterial DNA of these strains were detected by PCR to amplify the loci simultaneously with multiple variable number tandem repeat analysis(MLVA),and the clustering of genotypes was analyzed with BioNumerics(Version 4.5).Results Through MLVA,76 strains of multi-drug resistant Mycobacterium tuberculosis were divided into 3 genogroups,i.e.Ⅰ,Ⅱ,Ⅲ genogroup.The Ⅰgenogroup consists of 5 strains(6.6%),Ⅱgenogroup consists of 68 strains(89.5%),and Ⅲ genogroup consists of 3 strains(3.9%).At the strain level,19 isolates were categorized into 7 clusters,each cluster including 2-4 strains,and the clustering strains were collected from the same county or different county.Conclusion The strain of Ⅱ genogroup is the main epidemic strain in Fujian province,and some genotypes of strains spread recently in some county,even spread across counties.We should strengthen the control of drug resistant tuberculosis.