Local germplasm of high-yielding traditional cultivars and open-pollinated (OP) progenies of sweetpotato [Ipomoea batatas (L.)] were screened for drought tolerance in swidden and postrice conditions in the Phillipine highlands. Several clones from OP progenies and traditional cultivars showed some drought tolerance based on the yields of marketable storage roots. Under swidden conditions, the local cultivar Tokano, had the highest yield. Likewise, the traditional cultivar Kalbo-oy, produced the best yields in post-rice paddies. To obtain genetic markers that will be used in future breeding, genetic diversity analysis was performed. Genomic deoxyribonucleic acid (DNA) from seven sweetpotato genotypes, selected from those which produced storage roots under drought conditions, was subjected to Random Amplified Polymorphic DNA (RAPD) analysis. Twenty decamer primers were tested and 16 yielded DNA-amplification products. Among the 97 scored bands, 77 were polymorphic (79.38%). Genotype-specific DNA markers were also identified. The pairwise marker difference between genotypes ranged from 0.378 to 0.936, indicating a broad range of genetic diversity. A phenogram of the genetic relationships among those genotypes is presented.