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Molecular markers are powerful tools, which help in differentiating plant varieties at the DNA level and have been widelyused for genetic diversity studies in a number of crop species'. Understanding the genetic diversity of available clones of S.officinarum and S. spontaneum will be helpful in breeding programs. In the present study, a set of 48 sugarcane clones fromNational Hybridization Garden, Sugarcane Breeding Institute, Coimbatore was subjected to genetic diversity analysisinvolving 40 SSR markers of sugarcane and rice. SSR analysis involving a set of 20 sugarcane and 20 rice primer pairsgenerated 147 and 114 markers with average polymorphism information content (PIC) value of 0.665 and 0.532respectively. Cluster analysis using rice marker across 48 genotypes revealed two major clusters with ISH 23 remaining adeviant from the rest of the cultivars. Cluster analysis based on sugarcane SSR markers were found to be more or lesssimilar to that based on rice SSR markers showing minor difference in grouping. Hence, similar results obtained forcharacterizing the sugarcane clones by using SSR markers from sugarcane and rice reveal that markers with betterdiscriminating power from other cereals can bring out better characterization of sugarcane clones.