Identification of duplicates is essential for clonally propagated crop genebank management. The sensitivity and efficiency of Random Amplified Polymorphic DNA (RAPD) for duplicate identification in sweet potato was assessed in this study. The intervarietal variation in sweet potato was easily revealed by RAPD analysis. A combination of a few informative primers created a variety specific RAPD pattern, which unambiguously distinguished all tested varieties. The RAPD pattern also clearly verified all 'suspected' duplicate accessions of the same variety which shared similar morphological characters. Using 125 RAPD markers, we could not detect any intravarietal variation in either of the two common US varieties with its clones collected from 3 different sources. Moreover, when RAPD was applied to a transgenic Japanese clone with an intro-GUS gene and its non-transgenic control, it failed to reveal the intra-varietal difference, although the transonic clone has an obvious and inheritable dwarf symptom. These results demonstrated that RAPD fingerprinting is highly sensitive and efficient when verifying morphologically identical duplicate sweet potato accessions of the same variety. However, RAPD markers are non-sensitive and inefficient for detecting intravariety variation or somaclonal variation in sweet potato.