India has the unique distinction of having perhaps the largest diversities, both biological and cultural. The Nilgiri Hills of southern India, a home for several tribal pockets representing different genetic isolates, provides a genetic wealth to understand human evolution. We have analyzed eight widely distributed polymorphic insertion/deletion loci (AluAPO, AluACE, AluD1, AluPLAT, AluPV92, AluFXIIIB, CD4 del and mtNUC) in 250 unrelated individuals from five tribal populations (Badaga, Irula, Kota, Kurumba, and Toda). All loci were highly polymorphic except the CD4 del locus, at which the deletion allele was fixed in Kotas and Kurumbas. The levels of average heterozygosities were found to be high in all the populations. In most populations, they were also higher than those predicted by the island model of population structure. The gene diversity (GST = 8.3%) was found to be higher than that in populations of most global regions with the exception of Africa. It is clear from the present study that drift effects could have accentuated the process of genetic differentiation of the tribal populations. The possibility of an early demographic expansion of modern humans within south India also cannot be ruled out.