Epigenetic regulation plays an important role in the management of plant growth and development, and several reports have indicated that DNA methylation plays a critical role in seed development and viability. Michalak et al. study mature seeds of oak, Quercus robur, and find that an ageing-related decrease in total 5-methylcytosine during storage of recalcitrant seeds is highly and significantly correlated with a decrease in seed viability. Moreover, a significant difference is demonstrated between DNA methylation dynamics in orthodox and recalcitrant seeds. These findings advance our understanding of the mechanisms underlying the differences between the viability of recalcitrant and orthodox seeds during storage.