Multidrug-resistant S. Typhi declined with increase in nalidixic acid and ciprofloxacin resistance during 1998–2012. H58 haplotype was detected in majority of strains associated with either multidrug and/or fluoroquinolone resistance. Multidrug-resistant strains with or without plasmid shared the same set of resistance genes. Fluoroquinolone resistance was mediated by quinolone resistance-determining region mutation(s) in gyrA and parC genes. Pulsed-field gel electrophoresis showed more diversity among nalidixic acid-resistant strains than multidrug-resistant strains.