The global decline of species and habitats makes ex situ cultivation in botanical gardens becoming increasingly important. Most of the cultivated taxa are, however, held in a small number of individuals which may cause genetic depletion. Thus, I compared genetic structure and diversity of in situ and ex situ populations and tested possible determining factors like population size and the duration of cultivation. I analyzed these aspects for 6 arable plant species as arable plants are among the most threatened species groups in Central Europe. Results indicate genetic depletion in ex situ populations. However, there was hardly any effect of population size or duration of cultivation. For in situ populations genetic diversity was low and genetic structures were pronounced of the rare and threatened arable plant species.