Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease (JD) in animals, has also been linked with Crohn's disease in human beings. Lack of indigenous diagnostics and vaccine hampered control of JD in India. Designing effective control strategies require thorough understanding of the etiological agent at phenotypic and molecular levels. On the basis of cultural phenotypes and IS1311 PCR-REA typing, MAP strains have been genotyped as 'Cattle type', 'Sheep type' and 'Bison type'. Information exists on genetic differences and comparative evolution of 'Cattle type' and 'Sheep type' strains after divergence from M. avium; however, emphasis has been little on 'Bison type' strains. Recently, a new 'Indian Bison type' genotype has been reported as principal strain infecting different animal species and human beings in India. The study analyzed few genetic markers to have inferences on the molecular evolution of native MAP isolates belonging to 'Bison type' genotype. Results pointed towards recent evolution of 'Bison type' genotype.