Historically group G streptococcus (Streptococcus dysgalactiae subsp equisimilis, SDSE) has been considered a commensal organism, only causing of opportunistic infections. Multiple studies have now shown SDSE to be the cause a spectrum of disease similar to group A streptococcus (GAS), including pharyngitis, invasive disease and PSGN. Circumstantial evidence also exists for a role for SDSE in rheumatic fever. In contrast to GAS, our knowledge of the epidemiology, molecular genetics and pathogenesis of SDSE is limited. Here we describe a comparative genomic analysis of 240 SDSE genomes, representing 40 different SDSE emm-types, collected from different geographic regions. Phyogenetic analysis divided the genomes into 18 different genomic clusters. While individual emm-types and genome clusters were largely concordant, evidence for recombination involving this gene was apparent. Our data also show a strong correlation between genome cluster and the expression of group C or group G carbohydrate in SDSE. When compared to GAS, the genome structure is largely consistent, with differences largely attributable to the presence of mobile genetic elements. Together this data suggests underscore the value of population genomic analyses in providing new insights into the biology of SDSE.