The genetic profiles for 15 autosomal microsatellite loci were analyzed in a Tamil population from Southern India to study the genetic diversities and relatedness of this population with other national and global populations. Statistical analyses of the data revealed all loci were within Hardy–Weinberg Equilibrium (HWE) expectations with the exception of the locus D5S818 ( p = 0.011). A significantly greater inter-individual variation (Fst = 99%) observed within the individuals among the four subgroups in this study and low population differentiation (Fst = 1%) suggests relative genetic closeness of these four subgroups. This indicates that the populations in the southern region of India might have a common ancestry or probably experienced high gene flow during the period of their coexistence. The Neighbor Joining tree derived from genetic distances of samples from this study and other national and global populations show clustering of all the Indian populations in one branch of the tree while the African and Middle Eastern populations cluster in a separate branch. Principal Co-ordinate Analysis of the genetic distance data show clustering similar to the NJ tree.