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Objective: To preliminarily understand the genotyping characteristics regarding the variable number tandem repeats (VNTR) of Mycobacterium tuberculosis clinical isolates so as to provide evidence for the development of tuberculosis control and prevention programs in Fujian province., Methods: Fifteen VNTR locus sets were used to detect the clinical isolates from the fifth surveillance project on tuberculosis resistance, in Fujian province. BioNumerics version 4.5 were used to analyze the cluster from the results generated by genotyping., Results: 313 Mycobacterium tuberculosis isolates were divided into 9 clusters, including I, II, III, IV, V, VI, VII, VIII and IX, with the number of 220, 9, 48, 2, 1, 3, 10, 10, 10 isolates, respectively. Cluster I was the major lineage, accounting for 70.3% (220/313) of the total. Resistance rates of cluster I isolates to isoniazid, streptomycin, ethambutol and multi-drug-resistant were not statistically different from other clusters (P > 0.05). However, resistance rate to rifampicin (RFP) was significantly higher than that of other isolates of the clusters, 33.2% (73/220) vs. 20.4% (19/93) (P < 0.05)., Conclusion: The strains isolated from Fujian province showed significant polymorphism on genotyping. Cluster I seemed to be the dominant, calling for the close monitoring program on cluster I strains., Results: from our initial studies demonstrated the existence of significant correlation between cluster I strains and drug resistance to RFP.