A scarlet fever outbreak occurred in Hong Kong in 2011. The majority of cases resulted in the isolation of Streptococcus pyogenes emm12 with multiple antibiotic resistances. The second most common clinical serotype was emm1. The main objective of this study is to examine the microevolution of the emm12 and emm1 lineages associated with the outbreak. We sequenced the genomes of 57 emm12 and 11 emm1scarlet fever outbreak isolates and an additional with 90 temporally and geographically matched isolates not associated with scarlet fever. Phylogenetic analysis suggests that the emm12 outbreak was multi-clonal. Novel mobile genetic elements distributed across the major lineages include integrative conjugative-like elements encoding tetracycline and macrolide resistance, and prophage encoding the superantigens SSA, SpeC, and the DNase Spd1. The acquisition of these elements were predicted to have occurred independently across the lineages between the late 1980s and early 1990s. Whole genome principle component analyses are currently being employed to identify clinical-genomic associations. The multiclonal nature of the scarlet fever isolates suggests that multiple factors such as mobile genetic elements, environmental factors and host immune status may have contributed to the 2011 scarlet fever outbreak.