Sugarcane has acquired signifi cant importance in the world economy because of the sugar and ethanol production. Therefore, rapid multiplication of outstanding sugarcane variety is necessary in developing countries. The aim of this investigation was to compare regeneration effi ciency of various explants and genetic fi delity of regenerated plantlets certifi ed by using DNA-based molecular markers, that is, random amplifi ed length polymorphism (RAPD) and inter simple sequence repeats (ISSR). The sugarcane plantlets were obtained through direct (axillary buds, apical meristem, and leaf whorl disk) and indirect (callus culture) shoot organogenesis from the variety Co 86032. Among all the explants, highest shoot forming ability was observed in axillary buds showed 97.66±0.66% shoot formation and the highest number of shoots per explants (4.33±0.24) and a total number of regenerated shoots (173.00±8.11) were observed in the leaf whorl disk. Morphological variation was not observed among the regenerated plants from various explants and therefore, genomic DNA was isolated from fresh leaves and genetic fi delity assessment was carried out using RAPD and ISSR. Both the markers produced 1368 and 2271 bands, respectively, including all the tested plants, indicates that plants derived from direct organogenesis did not show any polymorphism. However, a genetic variation has been observed in the plants derived from callus and showed 4.54% polymorphism during analysis. The results suggested that plants regenerated from direct organogenesis are of more true-to-type, whereas genetic variation occurs during indirect organogenesis. Combination of RAPD along with ISSR can be used for detection of genetic variation in the early stage in sugarcane micropropagation. High performance of regeneration and low risk of genetic variation ascertains the effi ciency of this operation.