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The emergence of extensively drug-resistant tuberculosis (XDR-TB) in China is a great threat to TB control. To determine the molecular characterisation of XDR-TB isolates from China and the correlations between specific drug resistance-associated mutations and different genotype strains, 58 XDR-TB isolates were sequenced in eight drug loci, including katG , inhA , oxyR–ahpC intergenic region, rpoB , eis , rrs , gyrA and gyrB , and were genotyped using spoligotyping and analysis of the noise transfer function region. Compared with the phenotypic data, the sensitivities and specificities for DNA sequencing were 87.9% and 100.0% for isoniazid (INH), 91.4% and 98.3% for rifampicin (RIF), 60.4% and 100.0% for kanamycin (KAN) and 81.0% and 100.0% for ofloxacin (OFX), respectively. A combination of eight drug loci predicted XDR-TB phenotypes with 53.4% sensitivity (31/58 isolates) and 100.0% specificity. The most frequent mutations among these XDR-TB isolates were katG 315 and inhA -15 (for INH), 531, 526 and 516 in rpoB (for RIF), rrs 1401 and eis –10 (for KAN) and 94, 90 and 91 in gyrA (for OFX). Also, among these XDR-TB isolates, 44 (75.9%) were identified as Beijing genotype strain, of which 31 (70.5%) belonged to the modern Beijing sublineage. inhA -8, rpoB 526 and rpoB 531 mutations demonstrated significant statistical associations with ancient and modern Beijing family sublineage ( P < 0.05). However, Beijing and non-Beijing genotypes showed no association with specific resistance-conferring mutations. These results will be helpful in designing new molecular biology-based techniques to diagnose XDR-TB in China. [ABSTRACT FROM AUTHOR]