Genotypic differences have been used to characterize isolates of Mycobacterium avium subsp. paratuberculosis (Map), the agent of paratuberculosis in ruminants. These differences were up to 2 groups: Cattle type strains and sheep type strains. Polymerase chain reaction - restriction endonuclease analysis (PCR-REA) based on polymorphisms in IS1311 an insertion sequence present in Map and in Mycobacterium avium subsp. avium (Maa) in 7-10 copies. Techniques can be used as an easy and rapid method to distinguish between Maa and both cattle and sheep paratuberculosis strains. In the present study this IS1311 - PCR-REA typing method on the several of mycobacterial isolates from goats in India. Mycobacterium avium subsp. paratuberculosis isolated from India were identified as Bison type strains regardless of origin. These results led to the finding that strain different from sheep could be involved in these cases (cattle type) strain. However, molecular methods used in this study proved that they were B type strains only described before (Bison bison) from Montana, USA. Pending more extensive typing in other regions the results reported here establish an un-expected link between American Bison and Indian small ruminants. This is the first report of involvement of Bison type MAP strains in goat herds endemic for Johne's disease in India. This study also provides the genetic key to contradictory reports on the isolation of sheep strains and underlines the importance of using different strains for the diagnosis of Johne's disease