Background: For assessing the risk of escape of transgenes from cultivation, the persistence of feral populations of crop plants is an important aspect. Feral populations of oilseed rape, Brassica napus, are well known, but only scarce information is available on their population dynamics, particularly in Central Europe. To investigate genetic diversity, origin and persistence of feral oilseed rape in Austria, we compared variation at nine polymorphic microsatellite loci in eight feral populations with 19 commercial varieties. Results: Overall, commercial varieties and feral populations showed a similar pattern of genetic variation and a similar level of observed heterozygosity. The two groups, however, shared less than 50% of the alleles and no multilocus genotype. A significant among-group (commercial varieties versus feral populations) component of genetic variation was observed (AMOVA: F-CT = 0.132). Pairwise comparisons between varieties and feral populations showed moderate to very high genetic differentiation (F-ST = 0.209 - 0.900). The software STRUCTURE also demonstrated a clear separation between commercial varieties and feral samples: out of 17 identified genetic clusters, only one comprised plants from both a commercial variety and feral sites. Conclusions: The results suggest that feral oilseed rape is able to maintain persistent populations. The feral populations may have derived from older cultivars that were not included in our analyses or perhaps have already hybridised with related crops or wild relatives. Feral populations therefore have to be considered in ecological risk assessment and future coexistence measures as a potential hybridisation partner of transgenic oilseed rape.