The ability to improve productivity and agronomic traits of sweetpotato through breeding programs depends on assessing the genetic variation of their germplasm and genetic relationship to other genotypes. In addition, studying genetic diversity supports the conservation of genetic resources. In this study, three different DNA-based markers, random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and selective amplification of microsatellite polymorphic loci (SAMPL) were used for fingerprinting and detecting genetic variation for ten germplasm of sweetpotato. Results indicated that RAPD assays using 18 primers produced 213 bands, 145 of which were polymorphic with a percentage of 68.1%. AFLP using five primers yielded 344 amplified products with a percentage of 71.8% polymorphism. SAMPL using two primers combinations amplified 132 bands in which 85 being polymorphic representing 64.4%. Genetic relationship was estimated using Dice’s coefficient values between different accessions, ranging from 0.655 to 0.939 in RAPD, 0.749 to 0.936 in AFLP, and 0.742 to 0.928 for SAMPL. The UPGMA algorithm was used for grouping all germplasm based on their genetic distances. In total, the three molecular marker systems were compared on the basis of multiplex ratio, marker index and average heterozygosity and revealed that AFLP was the bestsuited molecular assay for fingerprinting and assessing genetic relationships. All analysis confirmed the relatively high genetic diversity present in sweetpotato germplasm used. Also, distinct DNA fingerprinting profile could be obtained with all the three molecular marker systems. These results clearly indicate the usefulness of DNA fingerprinting for the identification of sweetpotato germplasm, and their potentiality to eliminate accessions duplicates from gene banks around the world.

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