An outbreak of clinical mastitis was observed in dairy goats due to the zoonotic pathogen Streptococcus equi ssp. zooepidemicus. Affected goats were culled to prevent transmission of infection to other animals or humans. The objective of the study was to determine whether horses on the same farm were the source of the pathogen. Streptococcus equi ssp. zooepidemicus was obtained from milk of 10% of goats in the herd and from feces of 3 of 7 healthy horses that shared pasture and housing with the goats. Isolates of caprine and equine origin had identical biochemical profiles, including the ability to ferment sorbitol and lactose, which distinguishes S. equi ssp. zooepidemicus from S. equi ssp. equi. Sequencing of the 16S-23S intergenic spacer region and results from sodA-seeI multiplex PCR supported identification of isolates as S. equi ssp. zooepidemicus. Based on random amplified polymorphic DNA typing and rpoB and sodA sequencing, caprine isolates were indistinguishable from each other, but distinct from equine isolates. Further analysis of equine fecal samples showed that multiple strains of S. equi ssp. zooepidemicus can be present in a single sample or in sequential samples obtained from a single horse. Failure to detect the mastitis-causing strain in equine feces may indicate that horses were not the source of the mastitis outbreak in goats. Alternatively, the outbreak may be due to presence of multiple S. equi ssp. zooepidemicus strains in equine feces and a failure to detect all strains when analyzing a limited number of isolates per sample.