In flowering plants, specialized stem cells in floral meristems undergo meiosis and give rise to multicellular gametophytes. The epigenetic control of these developmental transitions is poorly understood, but likely involves multiple reprogramming events during meiosis and gametogenesis. Epigenome profiling of Arabidopsis meiocytes, uninucleate microspores and the two differentiated nuclei in mature pollen has shown that epigenetic reprogramming in the male germline is characterized by a widespread loss of non-CG methylation during meiosis and pollen mitosis, only to be restored in the seed after fertilization via small RNA activity. Comparisons with the methylomes and small RNA profiles of Arabidopsis cell cultures indicate that DNA methylation dynamics in pollen nuclei reflects their cell cycle stage. I will discuss our current model to explain how loss of non-CG methylation during the plant cell cycle promotes germline reprogramming and epigenetic variation in plants propagated as clones.