Genomic DNA of twenty four accessions belonging to seven small millet species were analyzed for RAPD, RFLP and AFLP profiles for a comprehensive understanding of the level of genetic diversity within the species and relationships between them. Thirty random primers generated a total of 115 amplification products of which 70 were polymorphic across all species.Twenty-five probe enzyme combinations were used for RFLP analysis that revealed 87 loci of which 62 were polymorphic across the species.AFLP analysis was done at inter-specific level using 12 primer combinations.This generated a total of 869 fragments of which 821 were polymorphic across the species analyzed. Species-specific AFLP profiles were obtained in 10 of the 12 primer combinations tested. It was noticed that the intra-specific variability in all the RAPD and RFLP marker systems was negligible. Species-specific polymorphic loci were observed for all the marker systems.The results are discussed in relation to the genetic relationship among the seven species analyzed.