A major scarlet fever outbreak occurred in Hong Kong in 2011. The majority of cases resulted in the isolation of Streptococcus pyogenes emm12 strains with resistance to multiple antibiotics. We sequenced the genomes of 52 emm12 scarlet fever outbreak isolates and 49 temporally and geographically matched emm12 isolates not associated with scarlet fever. A further 40 emm12 strains isolated up to 5 years prior to the current outbreak were also included. Phylogenetic analysis suggests the outbreak was multiclonal, with three major lineages. Several clones (less than 50 SNP differences across the core genome) contained multiple scarlet fever isolates. Novel mobile genetic elements distributed across the major lineages, include a 64.9 kb integrative and conjugative element (ICE) encoding tetracycline and macrolide resistance, and a 46.4 kb prophage encoding the superantigens SSA and SpeC, and the DNase Spd1. These elements have also been acquired by other GAS emm types. The multiclonal nature of the emm12 scarlet fever isolates suggests that a number of factors, including mobile genetic elements, environmental factors and host immune status may have contributed to the upsurge of scarlet fever in the 2011 outbreak.