It is commonly found that effective population sizes of natural populations are much smaller than census sizes of plants and animals. However, theoretical studies have shown that factors rarely investigated empirically, like seed banks in plants and diapause in animals, may have profound influence on effective sizes. Here we investigate whether the presence of seed banks can explain the relatively high genetic variability observed in northern European Arabidopsis thaliana populations with small census sizes. We have genotyped three above- and below- ground cohorts in 27 Norwegian populations using single nucleotide polymorphism markers. Although the populations varied extensively in levels of variability within and between cohorts, standard genetic population measures were comparable to those obtained in previous studies on above-ground cohorts using microsatellite markers. Estimated effective population sizes are larger for total populations (containing both seed bank and above-ground cohorts for 1 year) compared to each of the cohorts considered separately. Using a conservative approach, we find that the effective sizes are larger than census sizes of local populations, and that the effective generation time is higher than 1 year (3–4 years, on average), making A. thaliana a perennial semelparous plant at many northern European localities.