A SYBR Green I-based real-time quantitative PCR assay was utilized using senX3-regX3 and IS6110 as targets to identify Mycobacterium tuberculosis in 135 clinical samples from southern Taiwan. The bacterial loads of true positive samples estimated in this assay ranged from 33 to 7.7 × 105 CFU/ml, whereas false negative samples ranged from 10 to 25 CFU/ml. The specificity and sensitivity were 100% and 88.5%, respectively. Moreover, a multiplex allele-specific PCR was applied to detect mutation at three major hot spots (affecting codons 516, 526 and 531) of the rpoBgene affecting resistance to rifampicin, as well as codon 315 of the katG gene (resistance to isoniazid). The mutation rates of rpoB and katG were 69.6% (32/46) and 45.7% (21/46), respectively. The dual-gene mutation (rpoB and katG) rate was 41.3% (19/46). Among the hot spots on the rpoBgene, the mutation rate for rpoB 531(17/46, 37%) was higher than that of rpoB 516 (10/46, 21.7%) and rpoB 526 (8/46, 17.4%). Furthermore, for the four codons assayed (rpoB 516, 526, 531, andkatG), 11 mutations were identified as single mutation (23.9%), 18 as double mutations (39.1%), 3 as triple mutations, and none as quadruple mutations. Our results reveal the prevalence of tuberculosis drug-resistant mutations occurring on rpoB and katG genes in southern Taiwan.