Objective: Characterization of novel 'Indian Bison Type' bio-type of Mycobacterium avium subspecies paratuberculosis (MAP) strain 'S5' (goat origin) was done through six MAP cultural filtrate proteins (CFPs) genes (MAP 1693c, MAP 2168c, MAP Mod D, MAP 85c, MAP Pep AN and MAP Pep AC) encoding for above six recombinant CFPs. Material and Methods: Six immunogenic MAP CFPs genes (1693c, 2168c, ModD, 85c, Pep AN and Pep AC) were cloned and were confirmed by restriction digestions and sequencing. Evolutionary Analysis of the six genes was done using phylogenetic tree constructions and Sequence Identity plot. Results and Discussion: Sequence analysis of six CFPs genes was studied extensively for their genetic composition, mutations and other variations in their open reading frames. Good percentage of homology has been found among the global biotypes/strains of the MAP along with the MAP strain 'S5' and a novel biotype (Indian Bison Type) of goat origin and other Indian isolates. Aligned sequences of the six genes have been submitted to NCBI. Genebank accessioned by following IDs (MG753462, MG753463, MG753464, MG753465, MG753466 and MG753467). However, certain insertions, deletions within the genes still required to be explored to identify the nature of the disease in Indian scenario with respect to genotypic influences in geographical entity. Mutations were observed in four genes of MAP 'S5' strain, 2168c, Mod D, Pep AN and Pep AC. Phylogenetic tree analysis of MAP 'S5' genes showed 1693c and 2168c genes were taxonomically distant, on contrary Mod D, Pep AN were located taxonomically closer, 85C was present as out group of the first branch and Pep AC slightly away. Conclusion: The study helped to understand molecular diversity and homology of CFPs genes of MAP 'S5' with other strains. Mutations may lead to modulations in the functions of the MAP metabolism thereby influencing the virulence and host response to the disease.