The group A Streptococcus (GAS) is an important pathogen responsible for a wide range of human diseases. Fibronectin binding proteins (FBPs) play important role in promoting GAS adherence and invasion of host cells. The gene prtF2 encodes a FBP and is contained in approximately 60% of GAS strains. In the present study we have examined 51 prtF2-positive GAS strains isolated from the Northern Territory of Australia and describe two genotypes of prtF2, which are mutually exclusive. Both genotypes have been previously identified in the literature as pfbp and fbaB. We show these genotypes map to the same chromosomal location within the highly recombinatorial fibronectin-collagen-T antigen (FCT) locus, indicating they have arisen from a common ancestor, and in this study these have been designated as the pfbp-type and fbaB-type. Phylogenetic analysis of 7 pfbp-types, 14 fbaB-types and 11 prtF2-negative GAS strains by pulsed-field gel electrophoresis (PFGE) produced 32 distinct PFGE38 patterns. Interpretation of evolution based on the PFGE dendrogram by parsimony suggests that the pfbp-type is of a recent origin compared to the fbaB40 type. Comparing multiple DNA sequences of pfbp and fbaB-types reveals a mosaic pattern for the amino terminal region of pfbp-types. The fbaB-type is generally conserved at the amino terminus but varies in the number of fibronectin binding repeats contained within the carboxy terminus. Our data also suggests a possible association of the pfbp-genotype with sof (84.2%) whilst the fbaB45 genotype was found in a majority of GAS strains negative for sof (90.6%) indicating these two prtF2 subtypes may be under different selective pressures.