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This study deals with the characterization of 10 populations of M. musculus from different geographical locations in India. The genetics of Indian wild mice has been completely obscure and this is the first report on allozyme variations in the natural population. We have used a set of 24 biochemical genetic markers to measure levels of diversity within and among populations. The allelic frequency data indicate extreme genetic variability, which is further enhanced by the presence of novel alleles. Overall the species shows a high level of heterogenity. The highly polymorphic central populations of M. musculus cannot be assigned to any one particular subspecies. The allelic profiles, however, indicate a gradual differentiation toward the castaneus and batcrianus subspecies lineages.