The IS1311 polymerase chain reaction-restriction endonuclease analysis was used to detect genetic differences among 38 Mycobacterium avium subsp. paratuberculosis (Map) isolates from cattle, sheep, goats and bison from distinct regions of Spain, India and the United States of America (USA). In Spain, all eight bovine isolates, three out of six caprine isolates and one of ten ovine isolates were of the C type, while the other nine ovine isolates and three caprine isolates were of the S type. In India, all five ovine isolates and six caprine isolates were of the B type, and so were all three isolates from bison (Bison bison) from the USA. These results show that there are genetic differences between Map isolates related to geographic and host factors that have a potential use in the epidemiological tracing of new paratuberculosis isolates.