A common effort among members of the Association of Potato Inter-Genebank Collaborators (APIC) has yielded a global inventory of wild potato genetic resources that is freely accessible to researchers and breeders. In that database there are a number of accessions that originated from distributed progeny of a single original germplasm collection. The logical assumption has been that although these samples are in different locations, they should be genetically equivalent. This study tests this hypothesis by comparing 17 pairs of accessions of 16 different potato species, which are reputed duplicates preserved in the potato genebanks of The International Potato Center (CIP) in Peru and of the U.S.A. (USPG). The RAPD marker analysis revealed that even though the average genetic similarity of reputed duplicates was quite Ugli, there were a few with significant differences. Similarly, SSR markers identified three reputed duplicates that were genetically different. SSBs revealed a loss of markers for some inter-genebank comparisons, a probable indication of genetic drift. Duplicate potato collections between CEP and USPG are in most cases genetically identical. The few exceptions merit further investigation regarding causes and the impact on useful traits.