We have analysed nine autosomal STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) in Goud and Padmashali populations belonging to Chittoor and Cuddapah districts of Andhra Pradesh, India, respectively. This data was compared with the available data on Indian populations. Heterozygosity (H), power of discrimination (PD), probability exclusion (PE), typical paternity index (TPI), polymorphism information content (PIC), exact test with Bonferroni corrections and Arlequin analysis were carried out. Average heterozygosity observed in Goud and Padmashali populations were 0.82 and 0.81, respectively. Similarly, PD, PE, TPI and PIC have been found to be almost same between these two populations. Overall data analysis suggests the existence of sub-structuring in Indian populations.