The genetic structure of β-haemolytic Lancefield group C streptococci isolated from horses in Australia was examined by multilocus enzyme electrophoresis. The 249 isolates comprised 70 classified phenotypically as Streptococcus equi subspecies equi, 177 classified as S equi subspecies zooepidemicus and two which were unclassifiable. Forty-one electrophoretic types were identified which could be classified into three major clusters, A, B and C. Of the isolates, 178 fell into cluster B (types 4 to 22) and lay within a genetic distance of 0·36. Sixty-nine of the 70 S equi subspecies equi isolates fell into type 12, which suggests that they were members of a single clone, and the isolates from abscesses were significantly more likely to belong to type 12 than those from horses with no clinical signs (P<0·001). There were no other significant associations between electrophoretic types or clusters and the isolation of the organism from particular sites. These data suggested that S zooepidemicus may be the archetypal species from which the clone designated subspecies equi has been derived. If isolates of the subspecies equi from other geographical regions also prove to be members of electrophoretic type 12, this hypothesis would be strengthened.