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Potato wild relatives are important sources of novel variation for the genetic improvement of the cultivated potato. Consequently, many natural populations have been sampled and were deposited as accessions in gene banks around the world. Here we investigate to what extent the genetic variation of Bolivian wild potato species is maintained under gene bank conditions and how this diversity relates to that of current in situ populations. For this purpose, materials from seven potato species were screened for microsatellite variation. Genetic changes between different generations of ex situ germplasm were not observed for Solanum leptophyes and S. megistacrolobum, but were detected for S. neocardenasii and S. okadae, while each of the species S. acaule, S. avilesii and S. berthaultii showed stability in some cases and genetic change in others. The observed changes were ascribed to genetic drift and contamination resulting from human error during regeneration. Re-collected populations of six of the studied species showed highly significant genetic differences with the ex situ accessions that, apart from changes during ex situ maintenance, are most likely to be attributed to sampling effects during collecting and in situ genetic changes over time. The implications of the results for ex situ and in situ conservation strategies of wild potato species are discussed.