The Beijing genotype of Mycobacterium tuberculosis has frequently been found to be associated with drug resistance. Mutation analysis of the genes encoding 16S rRNA (rrs) and ribosomal protein S12 (rpsL) revealed a high frequency (97/102; 95.1%) of alterations in streptomycin-resistant M. tuberculosis isolates from Singapore, with rpsL K43R being the most common rpsL mutation (82/92; 89%), which was significantly associated with Beijing strains compared to non-Beijing strains (odds ratio = 10.88, 95% confidence interval = 3.48-34.1). This is the first study to report the association of Beijing strains with the rpsL K43R mutation in STR-resistant M. tuberculosis isolates with de novo resistance, as determined by clustering analysis.