Fecal samples of 708 domestic and 27 wild ruminants from seven districts of three states submitted to Microbiology Laboratory from 2004 to 2008 were screened for the presence and genotype diversity of Mycobacterium avium subspecies paratuberculosis (MAP) stusing modified microscopic examination and culture tests. MAP colonies were characterized and genotyped by IS900 PCR and IS1311 PCR-REA, respectively. In microscopic examination and culture, 18.7 and 31.2% sampled were positive, respectively. Percent positivity varied in different species and agro-climatic regions. Of the 151 DNA recovered from 230 MAP isolates, 94.7% (143) and 5.2% (8) were genotyped as 'Indian Bison type' and 'Cattle type', respectively. Cattle and buffaloes were infected with both the genotypes, whereas goat and sheep were infected exclusively by 'Indian Bison type'. Study showed low diversity in MAP genotypes and 'Indian Bison type' was the predominant genotype shared by different species, breeds and agro-climatic regions.