Staphylococcus aureus subsp. anaerobius, a microaerophilic, catalase-negative bacteria, is the etiological agent of abscess disease, a specific chronic condition of sheep and goats, characterized by the formation of necrotic lesions that are typically located in superficial lymph nodes. In this study, molecular analysis including pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and accessory gene regulator (agr) typing was carried out on 94 S. aureus subsp. anaerobius strains isolated in different countries (79 were isolated from 35 outbreaks of the disease in Spain from 1981 to 2009, 9 were isolated in Italy, 3 in Denmark and 3 in Sudan). All of the 94 S. aureus subsp. anaerobius isolates examined belonged to one PFGE type, within which four minority subtypes were identified. Representative isolates of all PFGE subtypes as well of all countries belonged to the same sequence type (ST), ST1464, which was a singleton, and to the agr type II. Our results support the view that abscess disease is caused by a single bacterial clone worldwide. This bacterium has existed for at least a century and, thus, has undergone long-term small ruminant host restriction.