5-Methylcytosine is one major epigenetic modification which plays critical roles during development, cell differentiation and organogenesis. Recently, remarkable progress has been achieved in understanding the programming and inheritance of DNA methylation during early embryogenesis and gametogenesis in vertebrates. Studies have revealed that sperm DNA methylome can be stably inherited by early embryos in zebrafish. However, both paternal and maternal methylomes undergo dramatic demethylation and reprogramming during mammalian embryogenesis and germ cell development. Most germ-line imprinting control regions escape from demethylation during mammalian embryogenesis, but these regions are demethylated during primordial germ cell development.